PDB-4r4k: Crystal structure of a cystatin-like protein (BACCAC

ID or keywords:

Entry

Database: PDB / ID: 4r4k

Title

Crystal structure of a cystatin-like protein (BACCAC_01506) from Bacteroides caccae ATCC 43185 at 1.69 A resolution

PDB-4r4k: Crystal structure of a cystatin-like protein (BACCAC_01506) from ... (2)

Components

Uncharacterized protein

PDB-4r4k: Crystal structure of a cystatin-like protein (BACCAC_01506) from ... (3)

Keywords

PDB-4r4k: Crystal structure of a cystatin-like protein (BACCAC_01506) from ... (4)

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Cystatin-like fold / divergent member of PF14254 family (DUF4348) / Joint Center for Structural Genomics / JCSG /

PDB-4r4k: Crystal structure of a cystatin-like protein (BACCAC_01506) from ... (5)

Protein Structure Initiative / PSI-BIOLOGY

Function / hom*ology

Nuclear Transport Factor 2; Chain: A, - #410 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta /

PDB-4r4k: Crystal structure of a cystatin-like protein (BACCAC_01506) from ... (6)

ACETATE ION / Uncharacterized protein

Function and hom*ology information

Biological species

PDB-4r4k: Crystal structure of a cystatin-like protein (BACCAC_01506) from ... (8)

PDB-4r4k: Crystal structure of a cystatin-like protein (BACCAC_01506) from ... (9)

Bacteroides caccae (bacteria)

Method

PDB-4r4k: Crystal structure of a cystatin-like protein (BACCAC_01506) from ... (10)

X-RAY DIFFRACTION /

PDB-4r4k: Crystal structure of a cystatin-like protein (BACCAC_01506) from ... (11)

SYNCHROTRON /

PDB-4r4k: Crystal structure of a cystatin-like protein (BACCAC_01506) from ... (12)

MAD / Resolution: 1.69 Å

PDB-4r4k: Crystal structure of a cystatin-like protein (BACCAC_01506) from ... (13)

Authors

Joint Center for Structural Genomics (JCSG)

PDB-4r4k: Crystal structure of a cystatin-like protein (BACCAC_01506) from ... (14)

Citation

Journal: To be published
Title: Crystal structure of a hypothetical protein (BACCAC_01506) from Bacteroides caccae ATCC 43185 at 1.69 A resolution
Authors: Joint Center for Structural Genomics (JCSG)

History

Deposition	Aug 19, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 1, 2014	Provider: repository / Type: Initial release
Revision 1.1	Dec 24, 2014	Group: Structure summary
Revision 1.2	Nov 22, 2017	Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3	Jan 24, 2018	Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4	Feb 1, 2023	Group: Database references / Derived calculations Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

PDB-4r4k: Crystal structure of a cystatin-like protein (BACCAC_01506) from ... (18)

Download

PDBx/mmCIF format	4r4k.cif.gz	281.7 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r4/4r4k ftp://data.pdbj.org/pub/pdb/validation_reports/r4/4r4k	HTTPS FTP

Related structure data

Similar structure data	2ml6-d 3nru-4 3g7p-d 7a4y-2 2f3i-d 1men-1 1vfc-d 1s79-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) F&H Search Similarity search - hom*ologyF&H Search
Other databases	TargetTrack: JCSG-419289

Similar structure data

2ml6-d

3nru-4

3g7p-d

7a4y-2

2f3i-d

1men-1

1vfc-d

1s79-d

Search similar-shape structures by Omokage search (details)

F&H Search

Similarity search - hom*ologyF&H Search

Other databases

TargetTrack: JCSG-419289

PDB-4r4k: Crystal structure of a cystatin-like protein (BACCAC_01506) from ... (49)

Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

C: Uncharacterized protein

D: Uncharacterized protein

hetero molecules

88.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

	Theoretical mass	Number of molelcules
Total (without water)	88,057	27
Polymers	71,503	4
Non-polymers	16,554	23
Water	11,205	622

A: Uncharacterized protein

hetero molecules

defined by author
21.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

	Theoretical mass	Number of molelcules
Total (without water)	21,753	8
Polymers	17,876	1
Non-polymers	3,877	7
Water	18	1

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

B: Uncharacterized protein

hetero molecules

defined by author
21.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

	Theoretical mass	Number of molelcules
Total (without water)	21,724	6
Polymers	17,876	1
Non-polymers	3,849	5
Water	18	1

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

C: Uncharacterized protein

hetero molecules

defined by author
24 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

	Theoretical mass	Number of molelcules
Total (without water)	24,018	7
Polymers	17,876	1
Non-polymers	6,143	6
Water	18	1

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

D: Uncharacterized protein

hetero molecules

defined by author
20.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

	Theoretical mass	Number of molelcules
Total (without water)	20,562	6
Polymers	17,876	1
Non-polymers	2,686	5
Water	18	1

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Unit cell

Length a, b, c (Å)	107.355, 62.823, 115.349
Angle α, β, γ (deg.)	90.000, 106.570, 90.000
Int Tables number	5
Space group name H-M	C121

Protein , 1 types, 4 molecules ABCD

#1: Protein	Uncharacterized protein Mass: 17875.715 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides caccae (bacteria) / Strain: ATCC 43185 / Gene: BACCAC_01506 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A5ZF42

Non-polymers , 5 types, 645 molecules

PDB-4r4k: Crystal structure of a cystatin-like protein (BACCAC_01506) from ... (75)

PDB-4r4k: Crystal structure of a cystatin-like protein (BACCAC_01506) from ... (76)

PDB-4r4k: Crystal structure of a cystatin-like protein (BACCAC_01506) from ... (77)

PDB-4r4k: Crystal structure of a cystatin-like protein (BACCAC_01506) from ... (78)

PDB-4r4k: Crystal structure of a cystatin-like protein (BACCAC_01506) from ... (79)

#2: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-PEU / 2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56,59,62,65,68,71,74,77,80-HEPTACOSAOXADOOCTACONTAN-82-OL / PEG 8000 / Polyethylene glycol Mass: 1221.461 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C₅₅H₁₁₂O₂₈ / Comment: precipitant*YM
#4: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 622 / Source method: isolated from a natural source / Formula: H₂O

Details

Sequence details	THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 33-185 OF THE TARGET SEQUENCE.

Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

PDB-4r4k: Crystal structure of a cystatin-like protein (BACCAC_01506) from ... (104)

Sample preparation

Crystal	Density Matthews: 2.61 Å³/Da / Density % sol: 52.82 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 26.0% polyethylene glycol 8000, 0.2M lithium sulfate, 0.1M sodium acetate pH 4.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

PDB-4r4k: Crystal structure of a cystatin-like protein (BACCAC_01506) from ... (106)

SYNCHROTRON / Site:

PDB-4r4k: Crystal structure of a cystatin-like protein (BACCAC_01506) from ... (107)

SSRL

PDB-4r4k: Crystal structure of a cystatin-like protein (BACCAC_01506) from ... (108)

/ Beamline: BL9-2 / Wavelength: 0.91837,0.97946

Detector

Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 14, 2014 / Details: double crystal monochromator

Radiation

Monochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.91837	1
2	0.97946	1

Reflection

Resolution: 1.69→29.757 Å / Num. obs: 81133 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 23.881 Å² / R_merge(I) obs: 0.111 / Net I/σ(I): 6.96

Reflection shell

R_merge(I) obs: 0.015 / Diffraction-ID: 1

Resolution (Å)	Highest resolution (Å)	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	% possible all
1.7-1.76		1	45152	15524	98.4
1.76-1.83		1.4	47295	15781	99.2
1.83-1.91		2	45312	15173	98.5
1.91-2.02		3	51571	17212	98.6
2.02-2.14		4.4	44653	14886	98.5
2.14-2.31		5.8	48932	16252	98.6
2.31-2.54		7.3	46966	15570	99.3
2.54-2.9		10.1	47042	15581	99.3
2.9-3.66		14.9	47896	16043	98.7
	3.66	19.5	46251	15683	98.1

Phasing

Phasing	Method: MAD

PDB-4r4k: Crystal structure of a cystatin-like protein (BACCAC_01506) from ... (112)

Processing

Software

Name	Version	Classification
MolProbity	3beta29	model building
PDB_EXTRACT	3.1	data extraction
SHELX		phasing
SHARP		phasing
XSCALE		data scaling
REFMAC	5.7.0032	refinement
XDS		data reduction
SHELXD		phasing

Refinement

Method to determine structure:

PDB-4r4k: Crystal structure of a cystatin-like protein (BACCAC_01506) from ... (114)

MAD / Resolution: 1.69→29.757 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.955 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 4.208 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.098
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. POLYETHYLENE GLYCOL (PEU), SULFATE (SO4) AND GLYCEROL (GOL) FROM THE CRYOPROTECTANT AND FROM THE CRYSTALLIZATION CONDITION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 4. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 5. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2026	4046	5 %	RANDOM
R_work	0.1752	-	-	-
obs	0.1765	80945	99.05 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso max: 116.68 Å² / B_iso mean: 29.6425 Å² / B_iso min: 11.48 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.4 Å²	0 Å²	0.27 Å²
2-	-	-0.13 Å²	-0 Å²
3-	-	-	-0.3 Å²

Refinement step

Cycle: LAST / Resolution: 1.69→29.757 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4916	0	199	622	5737

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.02	5488
X-RAY DIFFRACTION	r_bond_other_d	0.007	0.02	5061
X-RAY DIFFRACTION	r_angle_refined_deg	1.413	1.984	7409
X-RAY DIFFRACTION	r_angle_other_deg	1.348	3	11838
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.219	5	674
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.401	25.739	284
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.066	15	934
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.445	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	760
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	6124
X-RAY DIFFRACTION	r_gen_planes_other	0.007	0.02	1194
X-RAY DIFFRACTION	r_mcbond_it	2.667	4.045	2503
X-RAY DIFFRACTION	r_mcbond_other	2.658	4.033	2498
X-RAY DIFFRACTION	r_mcangle_it	3.921	7.544	3142

LS refinement shell

Resolution: 1.695→1.739 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.355	262	-
R_work	0.3	5286	-
all	-	5548	-
obs	-	-	92.71 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.266	0.0587	-0.2936	0.297	0.049	0.4779	-0.0208	0.0016	0.0136	-0.0467	0.0269	-0.0262	-0.0158	-0.0597	-0.0061	0.0384	0.0263	-0.0134	0.0543	-0.0221	0.0132	12.4736	10.9782	8.4868
2	0.395	-0.0291	-0.2479	0.8077	-0.0253	0.1628	0.0355	-0.0421	0.0384	0.0007	-0.0199	0.0263	-0.0099	0.026	-0.0155	0.0311	-0.0082	-0.0029	0.0205	-0.0076	0.043	29.9006	35.239	31.6767
3	0.201	-0.0713	0.0688	0.3219	-0.0025	0.242	0.0481	-0.0039	-0.0306	-0.0236	-0.0579	-0.0168	-0.0079	-0.0012	0.0097	0.0258	0.0129	-0.0092	0.0268	0.005	0.0442	30.7128	-1.1044	28.7857
4	0.4034	0.0558	0.0532	0.0509	0.1597	0.5716	0.0125	-0.0186	-0.0198	-0.0068	-0.0104	-0.0106	-0.0364	-0.0498	-0.002	0.0082	0.0119	-0.005	0.0416	-0.0219	0.0367	2.8186	22.5631	41.008

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	35 - 185
2	X-RAY DIFFRACTION	2	B	34 - 185
3	X-RAY DIFFRACTION	3	C	35 - 185
4	X-RAY DIFFRACTION	4	D	38 - 185

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PDB-4r4k: Crystal structure of a cystatin-like protein (BACCAC_01506) from ... (2024)