PDB-7v2b: Crystal Structure of VpsR display novel dimeric architecture and ...

ID or keywords:

Entry

Database: PDB / ID: 7v2b

Title

Crystal Structure of VpsR display novel dimeric architecture and c-di-GMP binding: mechanistic implications in oligomerization, ATPase activity and DNA binding.

Components

VpsR

Keywords

TRANSCRIPTION / X-ray crystallography / Biofilm / Fluorescence quenching / ATPase activity / second-messenger

Function / homology

Function and homology information

sequence-specific DNA binding / regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding
Similarity search - Function

Biological species

Vibrio cholerae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.2 Å

Authors

Chakrabortty, T. / Sen, U.

Funding support

India, 1items

Citation

Journal: J.Mol.Biol. / Year: 2022
Title: Crystal Structure of VpsR Revealed Novel Dimeric Architecture and c-di-GMP Binding Site: Mechanistic Implications in Oligomerization, ATPase Activity and DNA Binding.
Authors: Chakrabortty, T. / Roy Chowdhury, S. / Ghosh, B. / Sen, U.

History

Deposition	Aug 8, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 6, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7v2b.cif.gz	319.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7v2b.ent.gz	262.3 KB	Display	PDB format
PDBx/mmJSON format	7v2b.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7v2b_validation.pdf.gz	953.1 KB	Display	wwPDB validaton report
Full document	7v2b_full_validation.pdf.gz	979.6 KB	Display
Data in XML	7v2b_validation.xml.gz	30.5 KB	Display
Data in CIF	7v2b_validation.cif.gz	40 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v2/7v2b ftp://data.pdbj.org/pub/pdb/validation_reports/v2/7v2b	HTTPS FTP

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Related structure data

Related structure data	7v2vC 7v3wC 7v4eC 1ny5S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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: VpsR

D: VpsR

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: cross-linking, Size exclusion chromatography, DLS

Unit cell

Length a, b, c (Å)	118.639, 118.639, 78.255
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	144
Space group name H-M	P3₁

#1: Protein	VpsR Mass: 44722.109 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: vpsR / Plasmid: pet28a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9AQ41
#2: Chemical	ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₄P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.55 Å³/Da / Density % sol: 61.45 % Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: AMS(0.8M) Bicene pH 8.8 / PH range: 8-8.8

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 27, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97242 Å / Relative weight: 1
Reflection	Resolution: 3.2→47.34 Å / Num. obs: 65219 / % possible obs: 99.8 % / Redundancy: 3.2 % / CC_1/2: 0.812 / R_merge(I) obs: 0.087 / R_pim(I) all: 0.057 / R_rim(I) all: 0.105 / Net I/σ(I): 9.1
Reflection shell	Resolution: 3.2→3.31 Å / Redundancy: 3 % / R_merge(I) obs: 1.54 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2062 / CC_1/2: 0.329 / R_pim(I) all: 1.002 / R_rim(I) all: 1.851 / % possible all: 99.4

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1NY5

1ny5

Resolution: 3.2→47.273 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 0.1 / Phase error: 32.39 / Stereochemistry target values: ML
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns

	R_factor	Num. reflection	% reflection
R_free	0.2643	3615	9.85 %
R_work	0.214	-	-
obs	0.2191	20381	90.29 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.2→47.273 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5887	0	64	0	5951

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	6063
X-RAY DIFFRACTION	f_angle_d	1.05	8223
X-RAY DIFFRACTION	f_dihedral_angle_d	17.041	2271
X-RAY DIFFRACTION	f_chiral_restr	0.038	937
X-RAY DIFFRACTION	f_plane_restr	0.004	1051

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 (%)
3.2-3.2421	0.4384	143	0.4429	1296	X-RAY DIFFRACTION	92
3.2421-3.2865	0.4512	131	0.4041	1300	X-RAY DIFFRACTION	91
3.2865-3.3334	0.4615	141	0.3948	1299	X-RAY DIFFRACTION	93
3.3334-3.3832	0.3654	166	0.372	1353	X-RAY DIFFRACTION	91
3.3832-3.436	0.3603	132	0.3097	1238	X-RAY DIFFRACTION	91
3.436-3.4924	0.3532	142	0.2865	1264	X-RAY DIFFRACTION	92
3.4924-3.5526	0.2894	121	0.2836	1284	X-RAY DIFFRACTION	88
3.5526-3.6171	0.333	126	0.2841	1165	X-RAY DIFFRACTION	86
3.6171-3.6867	0.356	148	0.2793	1270	X-RAY DIFFRACTION	91
3.6867-3.7619	0.3679	145	0.2997	1259	X-RAY DIFFRACTION	88
3.7619-3.8437	0.3264	136	0.2966	1350	X-RAY DIFFRACTION	93
3.8437-3.933	0.3652	144	0.2686	1261	X-RAY DIFFRACTION	91
3.933-4.0313	0.2692	142	0.2522	1320	X-RAY DIFFRACTION	94
4.0313-4.1403	0.3062	116	0.259	1290	X-RAY DIFFRACTION	91
4.1403-4.262	0.3253	139	0.2359	1263	X-RAY DIFFRACTION	90
4.262-4.3995	0.2808	128	0.2203	1260	X-RAY DIFFRACTION	88
4.3995-4.5566	0.263	153	0.1999	1258	X-RAY DIFFRACTION	88
4.5566-4.7389	0.2765	124	0.2028	1235	X-RAY DIFFRACTION	88
4.7389-4.9544	0.2721	152	0.1917	1276	X-RAY DIFFRACTION	93
4.9544-5.2152	0.2275	134	0.2024	1309	X-RAY DIFFRACTION	92
5.2152-5.5415	0.2802	143	0.2278	1254	X-RAY DIFFRACTION	92
5.5415-5.9686	0.3138	137	0.2475	1272	X-RAY DIFFRACTION	88
5.9686-6.5679	0.2926	139	0.2379	1243	X-RAY DIFFRACTION	90
6.5679-7.515	0.2879	156	0.2053	1323	X-RAY DIFFRACTION	94
7.515-9.4556	0.205	130	0.1502	1223	X-RAY DIFFRACTION	86
9.4556-47.273	0.1666	147	0.1345	1232	X-RAY DIFFRACTION	89

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	8.4876	-2.1684	-3.6383	8.5055	-3.3451	8.7334	0.2471	-0.8963	0.6	0.4373	0.137	0.4536	-0.6147	0.4713	-0.2593	0.8213	-0.2063	-0.2125	1.0516	-0.2279	1.437	-97.5486	28.7251	5.1443
2	2.1304	0.732	-0.1387	4.4662	0.6261	-0.1879	0.3095	-0.6827	1.851	1.2223	0.1473	3.2837	-0.0365	0.0943	-0.2196	1.3587	-0.2975	0.0188	1.1997	0.2368	2.1851	-109.4328	18.7506	-4.824
3	2.4461	1.1176	-2.1043	4.6389	-1.0178	3.3921	-0.2864	0.2154	0.0928	-0.3252	0.1079	0.248	0.2776	0.0451	0.1601	1.0077	-0.2218	-0.3537	1.0221	0.2202	1.0728	-100.3987	-0.8577	-18.2839
4	4.5522	-4.2928	-4.7003	4.4908	4.6644	7.0131	0.5048	1.089	-1.026	-1.4659	0.4923	0.8998	-1.205	0.4348	-0.7908	1.6085	-0.2117	-0.1259	1.0233	0.321	2.0583	-97.4887	41.8541	-24.3946
5	3.9458	4.7421	-0.4207	6.1459	1.9473	9.0103	0.5903	-0.349	-0.1456	-0.7783	-0.1456	-0.0273	0.0062	0.3872	-0.8103	1.0841	-0.3015	-0.4593	1.1622	0.2195	1.9952	-94.892	29.6087	-22.1321
6	2.8632	3.0296	-0.3074	5.3398	0.094	2.677	0.1432	-0.014	1.192	-0.0136	0.59	1.6571	-0.4295	-0.168	-0.3779	1.0427	-0.2388	-0.258	1.0912	0.0162	1.8974	-103.2936	35.1643	-14.3403
7	3.6228	0.2918	-0.8656	2.808	-0.0423	3.8959	-0.3092	-0.4972	0.2673	0.2206	0.1434	-1.0071	-0.3118	0.7323	0.3657	0.8681	-0.1147	-0.2421	1.5778	-0.0764	1.4928	-73.5111	17.7042	-5.938
8	2.0572	-0.628	-1.7498	2.5059	1.044	2.754	-0.2776	-0.8925	-0.2762	-0.0419	0.4942	-0.366	0.5004	0.8747	-0.4119	0.7398	0.0431	-0.2574	1.542	-0.1725	1.2735	-68.6006	8.1199	-0.5686

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 113 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 114 through 164 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 165 through 382 )
4	X-RAY DIFFRACTION	4	chain 'D' and (resid 7 through 42 )
5	X-RAY DIFFRACTION	5	chain 'D' and (resid 43 through 83 )
6	X-RAY DIFFRACTION	6	chain 'D' and (resid 84 through 133 )
7	X-RAY DIFFRACTION	7	chain 'D' and (resid 134 through 207 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 208 through 382 )

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