PDB-3kop: Crystal structure of Protein with a cyclophilin-like fold (YP_831...

ID or keywords:

Entry

Database: PDB / ID: 3kop

Title

Crystal structure of Protein with a cyclophilin-like fold (YP_831253.1) from Arthrobacter sp. FB24 at 1.90 A resolution

Components

Uncharacterized protein

Keywords

Structural Genomics / Unknown function / Protein with a cyclophilin-like fold / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2

Function / homology

Protein of unknown function DUF3830 / Protein of unknown function (DUF3830) / Cyclophilin - #20 / Cyclophilin / Cyclophilin-like domain superfamily / Beta Barrel / Mainly Beta / Uncharacterized protein

Function and homology information

Biological species

Arthrobacter sp. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.9 Å

Authors

Joint Center for Structural Genomics (JCSG)

Citation

Journal: To be published
Title: Crystal structure of Protein with a cyclophilin-like fold (YP_831253.1) from Arthrobacter sp. FB24 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)

History

Deposition	Nov 13, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 24, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3	Jul 17, 2019	Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description Category: pdbx_distant_solvent_atoms / software / struct_conn Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3kop.cif.gz	215 KB	Display	PDBx/mmCIF format
PDB format	pdb3kop.ent.gz	178.3 KB	Display	PDB format
PDBx/mmJSON format	3kop.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3kop_validation.pdf.gz	482.5 KB	Display	wwPDB validaton report
Full document	3kop_full_validation.pdf.gz	489 KB	Display
Data in XML	3kop_validation.xml.gz	43.4 KB	Display
Data in CIF	3kop_validation.cif.gz	64 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ko/3kop ftp://data.pdbj.org/pub/pdb/validation_reports/ko/3kop	HTTPS FTP

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Related structure data

Similar structure data	2glm-d 3dp2-d 2vaf-1 5kn1-2 3dp0-d 4moc-1 5kn1-1 3b7j-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: 392654

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#163 - Jul 2013 HIV Capsid similarity (1) #245 - May 2020 Spliceosomes similarity (1)

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

C: Uncharacterized protein

D: Uncharacterized protein

E: Uncharacterized protein

F: Uncharacterized protein

126 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	69.294, 98.102, 84.503
Angle α, β, γ (deg.)	90.000, 93.190, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	2	A	1 - 169
2	1	1	2	B	1 - 169
3	1	1	2	C	1 - 169
4	1	1	2	D	1 - 169
5	1	1	2	E	1 - 169
6	1	1	2	F	1 - 169

#1: Protein	Uncharacterized protein Mass: 20942.668 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrobacter sp. (bacteria) / Strain: FB24 / Gene: Arth_1761 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A0JVT3
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 814 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.28 Å³/Da / Density % sol: 46.1 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 10.0000% MPD, 0.1M Acetate pH 5.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL11-1 / Wavelength: 0.91837,0.97963

Detector

Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 8, 2009 / Details: Flat mirror (vertical focusing)

Radiation

Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.91837	1
2	0.97963	1

Reflection

Resolution: 1.9→29.907 Å / Num. obs: 88263 / % possible obs: 99.5 % / Redundancy: 2.6 % / B_iso Wilson estimate: 18.599 Å² / R_merge(I) obs: 0.086 / R_sym value: 0.086 / Net I/σ(I): 9

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
1.9-1.95	2.5	0.498	2	16367	6518	0.498	100
1.95-2	2.5	0.399	1.9	16215	6414	0.399	99.9
2-2.06	2.5	0.313	2.4	15622	6195	0.313	100
2.06-2.12	2.5	0.302	0.9	15339	6075	0.302	100
2.12-2.19	2.5	0.224	3.4	14709	5797	0.224	99.9
2.19-2.27	2.5	0.215	1.3	14349	5664	0.215	99.9
2.27-2.36	2.5	0.173	4.3	13863	5442	0.173	99.9
2.36-2.45	2.6	0.143	5.2	13407	5245	0.143	99.8
2.45-2.56	2.6	0.126	5.9	12792	5008	0.126	99.7
2.56-2.69	2.6	0.111	6.2	12198	4782	0.111	99.6
2.69-2.83	2.6	0.089	8	11708	4564	0.089	99.5
2.83-3	2.6	0.08	8.5	11149	4330	0.08	99.4
3-3.21	2.6	0.071	8.9	10343	4029	0.071	99.2
3.21-3.47	2.6	0.057	10.5	9722	3773	0.057	99.2
3.47-3.8	2.6	0.047	12.8	8962	3462	0.047	98.8
3.8-4.25	2.6	0.041	12.6	8129	3136	0.041	98.6
4.25-4.91	2.6	0.036	16.2	7106	2731	0.036	98.2
4.91-6.01	2.6	0.037	16.2	6067	2334	0.037	98
6.01-8.5	2.6	0.045	13	4682	1797	0.045	97.5
8.5-29.91	2.6	0.041	12.3	2479	967	0.041	94.4

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Phasing

Phasing	Method: MAD

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0053	refinement
PHENIX		refinement
SOLVE		phasing
MolProbity	3beta29	model building
SCALA	3.2.5	data scaling
PDB_EXTRACT	3.006	data extraction
MOSFLM		data reduction

Refinement

Method to determine structure:

MAD / Resolution: 1.9→29.907 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.939 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 6.209 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.121
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 ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.196	4416	5 %	RANDOM
R_work	0.16	-	-	-
obs	0.162	88235	99.3 %	-

Solvent computation

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

Displacement parameters

B_iso max: 58.83 Å² / B_iso mean: 19.821 Å² / B_iso min: 4.23 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.19 Å²	0 Å²	0.92 Å²
2-	-	-0.64 Å²	0 Å²
3-	-	-	-0.45 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→29.907 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7467	0	0	814	8281

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	7847
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	5095
X-RAY DIFFRACTION	r_angle_refined_deg	1.401	1.945	10769
X-RAY DIFFRACTION	r_angle_other_deg	0.909	3	12476
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.571	5	1029
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.551	24.33	358
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.239	15	1194
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.064	15	43
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	1233
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	8911
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1610
X-RAY DIFFRACTION	r_mcbond_it	0.671	1.5	4927
X-RAY DIFFRACTION	r_mcbond_other	0.18	1.5	1992
X-RAY DIFFRACTION	r_mcangle_it	1.245	2	7986
X-RAY DIFFRACTION	r_scbond_it	1.77	3	2920
X-RAY DIFFRACTION	r_scangle_it	2.784	4.5	2748

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	864	TIGHT POSITIONAL	0.08	0.2
2	B	864	TIGHT POSITIONAL	0.08	0.2
3	C	864	TIGHT POSITIONAL	0.13	0.2
4	D	864	TIGHT POSITIONAL	0.08	0.2
5	E	864	TIGHT POSITIONAL	0.09	0.2
6	F	864	TIGHT POSITIONAL	0.12	0.2
1	A	941	MEDIUM POSITIONAL	0.16	1
2	B	941	MEDIUM POSITIONAL	0.15	1
3	C	941	MEDIUM POSITIONAL	0.21	1
4	D	941	MEDIUM POSITIONAL	0.13	1
5	E	941	MEDIUM POSITIONAL	0.12	1
6	F	941	MEDIUM POSITIONAL	0.21	1
1	A	864	TIGHT THERMAL	0.14	0.5
2	B	864	TIGHT THERMAL	0.16	0.5
3	C	864	TIGHT THERMAL	0.2	0.5
4	D	864	TIGHT THERMAL	0.2	0.5
5	E	864	TIGHT THERMAL	0.17	0.5
6	F	864	TIGHT THERMAL	0.15	0.5
1	A	941	MEDIUM THERMAL	0.14	1
2	B	941	MEDIUM THERMAL	0.14	1
3	C	941	MEDIUM THERMAL	0.19	1
4	D	941	MEDIUM THERMAL	0.17	1
5	E	941	MEDIUM THERMAL	0.17	1
6	F	941	MEDIUM THERMAL	0.15	1

LS refinement shell

Resolution: 1.9→1.949 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.283	300	-
R_work	0.256	6200	-
all	-	6500	-
obs	-	-	99.72 %

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	0.597	0.0278	-0.3223	0.6944	-0.1123	0.6325	0.0175	-0.0207	0.0481	0.0374	-0.0163	-0.045	-0.064	0.0624	-0.0011	0.0255	-0.0202	0.0094	0.0176	-0.0063	0.0204	25.0129	42.4211	15.0744
2	0.3955	-0.1685	-0.3143	0.8127	-0.0684	0.8589	0.0001	0.0037	0.0159	0.0105	0.0048	0.0047	-0.0635	-0.038	-0.0048	0.0137	0.0008	0.0045	0.0048	-0.0037	0.006	-1.1963	37.6907	27.5187
3	0.4614	0.126	-0.0254	0.5716	-0.0125	0.6354	-0.0023	-0.0567	0.0144	0.0216	-0.0299	0.0089	0.0395	0.0067	0.0322	0.011	-0.002	0.0061	0.0078	-0.0027	0.0042	3.9108	2.0084	27.0556
4	0.9963	-0.3007	0.0895	0.8486	0.2316	0.7995	-0.0499	-0.2156	0.0107	0.1846	0.0585	-0.0877	-0.0437	0.0694	-0.0086	0.0605	-0.013	-0.0219	0.085	0.0005	0.0125	29.3361	23.284	39.6099
5	0.4725	0.0049	0.0056	0.807	-0.4361	0.6156	0.0374	0.0288	0.0099	-0.127	-0.0058	0.0581	0.0597	-0.0138	-0.0316	0.0272	0.0054	-0.0085	0.0034	0.0001	0.0044	1.1956	19.6405	1.674
6	0.6426	-0.0384	-0.0545	0.4601	0.1384	0.6737	0.0229	0.0111	-0.0306	-0.0175	-0.0146	-0.097	0.0234	0.0794	-0.0083	0.013	0.0092	0.013	0.0156	0.0081	0.033	30.3919	5.0075	13.3386

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 166
2	X-RAY DIFFRACTION	2	B	1 - 166
3	X-RAY DIFFRACTION	3	C	-6 - 166
4	X-RAY DIFFRACTION	4	D	0 - 165
5	X-RAY DIFFRACTION	5	E	-5 - 166
6	X-RAY DIFFRACTION	6	F	-16 - 166

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