PDB-4wai: Structural characterization of the late competence protein ComFB ...

ID or keywords:

Entry

Database: PDB / ID: 4wai

Title

Structural characterization of the late competence protein ComFB from Bacillus subtilis.

Components

ComF operon protein 2

Keywords

METAL BINDING PROTEIN / comF operon / late competence operon / DNA uptake / natural transformation / competent Bacillus subtilis

Function / homology

Late competence development protein ComFB / Late competence development protein ComFB / establishment of competence for transformation / ComF operon protein 2

Function and homology information

Biological species

Bacillus subtilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.427 Å

Authors

Sysoeva, T.A. / Bane, L.B. / Xiao, D. / Gaudet, R. / Burton, B.M.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	P41 GM103403	United States
Department of Energy (DOE, United States)	DE-AC02-06CH11357	United States

Citation

Journal: Biosci.Rep. / Year: 2015
Title: Structural characterization of the late competence protein ComFB from Bacillus subtilis.
Authors: Sysoeva, T.A. / Bane, L.B. / Xiao, D.Y. / Bose, B. / Chilton, S.S. / Gaudet, R. / Burton, B.M.

History

Deposition	Aug 29, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 10, 2014	Provider: repository / Type: Initial release
Revision 1.1	May 6, 2015	Group: Database references
Revision 1.2	Aug 23, 2017	Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary Category: diffrn_detector / diffrn_source ...diffrn_detector / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software / struct_keywords Item: _diffrn_detector.detector / _diffrn_source.pdbx_wavelength_list ..._diffrn_detector.detector / _diffrn_source.pdbx_wavelength_list / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _software.version / _struct_keywords.text
Revision 1.3	Sep 6, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Dec 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4wai.cif.gz	158.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4wai.ent.gz	127.9 KB	Display	PDB format
PDBx/mmJSON format	4wai.json.gz		Tree view	PDBx/mmJSON format
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Validation report

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

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Related structure data

Similar structure data	1tjd-d 5dc0-d 2yzq-d 1u41-2 1u36-1 4z5h-1 4it4-6 4it4-1 2az0-d 2cky-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: ComF operon protein 2

C: ComF operon protein 2

B: ComF operon protein 2

D: ComF operon protein 2

hetero molecules

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

1

A: ComF operon protein 2

B: ComF operon protein 2

hetero molecules

defined by software
27 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: ComF operon protein 2

D: ComF operon protein 2

hetero molecules

defined by software
27 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	41.483, 123.579, 41.759
Angle α, β, γ (deg.)	90.00, 93.92, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	ComF operon protein 2 Mass: 13447.466 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: comFB, comF2, BSU35460 / Production host: Escherichia coli (E. coli) / References: UniProt: P39146
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 1.99 Å³/Da / Density % sol: 38.04 %
Crystal grow	Temperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 22 % PEG 3350, 0.2 M NaCl, 0.1 M BisTris

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.427→34.543 Å / Num. all: 15878 / Num. obs: 14767 / % possible obs: 93 % / Redundancy: 3.1 % / R_merge(I) obs: 0.101 / Net I/σ(I): 6.18
Reflection shell	Resolution: 2.427→2.513 Å / Mean I/σ(I) obs: 1.39

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Processing

Software

Name: PHENIX / Version: 1.9_1692 / Classification: refinement

Refinement

Resolution: 2.427→34.54 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.12 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2509	1486	10.07 %
R_work	0.2077	-	-
obs	0.2122	14762	92.99 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.427→34.54 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2767	0	4	5	2776

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.014	2807
X-RAY DIFFRACTION	f_angle_d	1.181	3766
X-RAY DIFFRACTION	f_dihedral_angle_d	10.95	1062
X-RAY DIFFRACTION	f_chiral_restr	0.039	473
X-RAY DIFFRACTION	f_plane_restr	0.004	466

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.4267-2.505	0.3448	94	0.34	874	X-RAY DIFFRACTION	67
2.505-2.5945	0.3529	143	0.3092	1246	X-RAY DIFFRACTION	96
2.5945-2.6983	0.3081	126	0.3052	1242	X-RAY DIFFRACTION	97
2.6983-2.8211	0.3274	152	0.2896	1248	X-RAY DIFFRACTION	97
2.8211-2.9697	0.3222	154	0.2864	1249	X-RAY DIFFRACTION	97
2.9697-3.1557	0.3498	131	0.2675	1252	X-RAY DIFFRACTION	97
3.1557-3.3991	0.2887	153	0.2611	1239	X-RAY DIFFRACTION	96
3.3991-3.7408	0.2731	133	0.2128	1257	X-RAY DIFFRACTION	96
3.7408-4.2813	0.2101	138	0.1927	1228	X-RAY DIFFRACTION	96
4.2813-5.3906	0.2194	128	0.185	1238	X-RAY DIFFRACTION	94
5.3906-34.5463	0.2248	134	0.1617	1203	X-RAY DIFFRACTION	91

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	6.5973	-2.1378	2.3812	2.4734	-4.1125	5.2451	-0.0496	-0.2995	0.1143	1.3411	0.9773	-0.0189	-0.5112	0.2236	-0.8913	0.7298	-0.1046	0.0721	0.5545	-0.02	0.4546	60.4931	-33.4737	16.5345
2	4.9142	2.1038	0.3038	10.1875	-2.2653	8.1841	0.1061	0.1074	0.7671	-0.1398	0.0038	-0.3584	-1.2024	0.0272	-0.067	0.6079	-0.115	0.0396	0.5632	-0.0725	0.4971	55.0915	-28.8105	13.0089
3	2.1935	-2.5941	-0.8418	2.4171	-4.9624	2.1988	-0.06	0.7954	-0.6715	-0.0964	-0.0168	-1.2525	-0.7421	0.6199	-0.1849	1.0782	-0.0746	-0.1542	0.9921	-0.2052	0.8854	69.3413	-39.9335	17.3691
4	1.9695	9.7036	-7.656	4.9784	-6.8463	2.0078	-0.3199	-0.7503	1.4784	-0.6078	0.1579	-1.2294	1.4369	-1.1237	0.9828	1.8482	0.0766	-0.0777	1.2468	-0.2681	1.0421	72.6536	-29.9642	8.4346
5	2.8116	-1.423	0.8579	11.0109	6.6134	4.056	0.8098	1.0951	0.2499	-1.3076	-0.3206	-0.5083	-0.3851	0.273	-0.1054	0.7973	-0.0513	0.0154	0.6878	0.1395	0.4826	56.7479	-26.1119	5.6866
6	9.0377	-4.3396	-8.7274	2.3078	3.7398	8.6254	2.0864	0.728	0.028	-0.0195	-1.2151	0.7278	-1.2855	-0.3481	0.3208	1.2951	0.0986	-0.027	1.047	-0.3454	1.3642	40.6079	-19.6178	15.7504
7	3.1812	-1.4198	1.2042	2.3876	6.2353	6.408	-0.1615	-0.2247	-0.185	0.7681	0.197	-0.0084	0.2805	-0.2212	0.057	0.8176	-0.0751	0.1223	0.6205	0.1628	0.5319	64.7983	-29.264	37.2986
8	3.305	-6.3448	-0.4867	2.865	-1.6662	3.2928	0.0418	-0.756	-1.4892	1.713	0.2792	-0.1776	0.9469	0.4799	-0.2531	0.9741	-0.0147	-0.1974	0.7161	0.1042	0.8474	73.2089	-38.4513	33.8819
9	2.7598	-3.7761	-5.3261	7.3096	4.8164	3.0256	1.2271	-0.3436	0.1666	-0.4528	-0.1649	0.1216	-1.6308	-0.3815	-1.255	0.8931	-0.0044	0.2157	0.6638	0.0929	0.5249	65.7138	-21.0313	33.2374
10	9.7168	3.1067	1.482	2.4859	7.3691	9.4022	-0.2938	1.4432	0.1661	-1.3587	-0.0505	-0.0279	0.2762	-0.9624	0.5167	1.1478	-0.1241	0.0519	1.1907	0.1998	0.8193	55.0733	-25.7901	33.5762
11	2.3899	-1.8349	9.0064	8.4487	-2.6975	8.7942	-0.743	0.8287	-0.4133	-0.3582	0.4816	-0.5167	-0.5193	0.0746	0.3662	0.5081	-0.1145	0.0172	0.5189	-0.0366	0.5015	70.6665	-36.5444	26.5252
12	2.0193	1.5615	-1.3351	6.4343	4.6995	2.1116	1.4287	0.5449	-0.0051	-0.0074	1.5871	0.594	0.8316	0.4333	-1.8424	0.9237	0.2643	-0.1708	1.1823	0.1223	1.2105	86.4079	-40.2812	36.7728
13	4.3685	1.4158	-0.7304	2.4241	0.444	4.4476	-0.0658	-0.2638	-0.7026	0.6731	0.2671	1.3975	1.031	-0.8024	-0.1925	0.8189	-0.1995	0.085	0.686	0.0835	0.8066	46.8055	-49.9207	19.3037
14	5.5105	1.9494	-0.2637	4.0057	-0.5655	5.4757	0.3444	-0.2168	-0.7693	0.4211	-0.0569	0.4019	0.8507	0.0964	-0.2388	0.7617	-0.1696	-0.0124	0.5655	-0.0064	0.6538	53.8282	-50.6253	17.9592
15	0.5042	1.3462	-1.0745	4.9323	-4.0662	3.4009	0.7524	0.7926	-0.1928	-0.3168	-0.9792	-1.5956	-0.0921	-1.1518	0.6323	0.7519	0.0924	0.1496	1.674	0.1083	1.2724	38.2498	-40.4509	18.4824
16	6.6871	2.3708	1.6585	8.2144	-0.1986	4.4238	-0.4977	0.247	0.3292	0.3215	0.0916	-0.606	-0.0623	0.0437	0.1128	0.9138	0.0309	0.1227	0.5594	-0.0761	0.8121	52.4611	-56.8065	15.3475
17	4.1852	-0.0889	-0.9276	8.4824	1.5001	5.6004	-0.0079	-0.5725	0.7953	1.0617	0.1404	-0.3893	-0.1133	0.2067	-0.2286	0.9895	-0.1922	0.0755	0.6109	-0.0701	0.55	72.438	-11.4646	38.5894
18	4.5732	-4.5015	5.5137	4.1216	-5.2612	6.5517	-0.2648	-0.0359	1.8381	-1.698	-2.532	-4.6187	-1.2564	2.9355	1.9139	1.124	-0.0488	0.416	1.7316	0.0237	2.7085	86.3527	-14.2344	33.1773
19	3.1847	-3.5577	-3.6755	3.6715	5.7986	4.2587	1.0494	0.4065	0.065	0.0939	-0.7985	0.0147	-0.1788	-0.8446	-0.35	1.3116	-0.033	0.2411	0.6457	0.1217	1.2025	66.3495	-4.6313	34.7358

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 16 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 17 through 49 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 50 through 59 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 60 through 64 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 65 through 82 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 83 through 91 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 1 through 16 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 17 through 39 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 40 through 49 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 50 through 65 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 66 through 82 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 83 through 91 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 1 through 20 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 21 through 49 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 50 through 59 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 60 through 89 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 1 through 50 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 51 through 64 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 65 through 88 )

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