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

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Basic information

Entry
Database: PDB / ID: 7v2b
TitleCrystal Structure of VpsR display novel dimeric architecture and c-di-GMP binding: mechanistic implications in oligomerization, ATPase activity and DNA binding.
ComponentsVpsR
KeywordsTRANSCRIPTION / 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
VpsR domain / VpsR domain / Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / Sigma-54 interaction domain, ATP-binding site 1 / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type ...VpsR domain / VpsR domain / Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / Sigma-54 interaction domain, ATP-binding site 1 / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / Homeobox-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / VpsR
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsChakrabortty, T. / Sen, U.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)EMR/2015/000780 Dated 18-07-2016 India
CitationJournal: 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
DepositionAug 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VpsR
D: VpsR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4914
Polymers89,4442
Non-polymers1,0462
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, Size exclusion chromatography, DLS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7090 Å2
ΔGint-35 kcal/mol
Surface area35040 Å2
MethodPISA
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 number144
Space group name H-MP31

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Components

#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 / Guanosine 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 interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity 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 growTemperature: 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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 3.2→47.34 Å / Num. obs: 65219 / % possible obs: 99.8 % / Redundancy: 3.2 % / CC1/2: 0.812 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.057 / Rrim(I) all: 0.105 / Net I/σ(I): 9.1
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 3 % / Rmerge(I) obs: 1.54 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2062 / CC1/2: 0.329 / Rpim(I) all: 1.002 / Rrim(I) all: 1.851 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.2643 3615 9.85 %
Rwork0.214 --
obs0.2191 20381 90.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→47.273 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5887 0 64 0 5951
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046063
X-RAY DIFFRACTIONf_angle_d1.058223
X-RAY DIFFRACTIONf_dihedral_angle_d17.0412271
X-RAY DIFFRACTIONf_chiral_restr0.038937
X-RAY DIFFRACTIONf_plane_restr0.0041051
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.24210.43841430.44291296X-RAY DIFFRACTION92
3.2421-3.28650.45121310.40411300X-RAY DIFFRACTION91
3.2865-3.33340.46151410.39481299X-RAY DIFFRACTION93
3.3334-3.38320.36541660.3721353X-RAY DIFFRACTION91
3.3832-3.4360.36031320.30971238X-RAY DIFFRACTION91
3.436-3.49240.35321420.28651264X-RAY DIFFRACTION92
3.4924-3.55260.28941210.28361284X-RAY DIFFRACTION88
3.5526-3.61710.3331260.28411165X-RAY DIFFRACTION86
3.6171-3.68670.3561480.27931270X-RAY DIFFRACTION91
3.6867-3.76190.36791450.29971259X-RAY DIFFRACTION88
3.7619-3.84370.32641360.29661350X-RAY DIFFRACTION93
3.8437-3.9330.36521440.26861261X-RAY DIFFRACTION91
3.933-4.03130.26921420.25221320X-RAY DIFFRACTION94
4.0313-4.14030.30621160.2591290X-RAY DIFFRACTION91
4.1403-4.2620.32531390.23591263X-RAY DIFFRACTION90
4.262-4.39950.28081280.22031260X-RAY DIFFRACTION88
4.3995-4.55660.2631530.19991258X-RAY DIFFRACTION88
4.5566-4.73890.27651240.20281235X-RAY DIFFRACTION88
4.7389-4.95440.27211520.19171276X-RAY DIFFRACTION93
4.9544-5.21520.22751340.20241309X-RAY DIFFRACTION92
5.2152-5.54150.28021430.22781254X-RAY DIFFRACTION92
5.5415-5.96860.31381370.24751272X-RAY DIFFRACTION88
5.9686-6.56790.29261390.23791243X-RAY DIFFRACTION90
6.5679-7.5150.28791560.20531323X-RAY DIFFRACTION94
7.515-9.45560.2051300.15021223X-RAY DIFFRACTION86
9.4556-47.2730.16661470.13451232X-RAY DIFFRACTION89
Refinement TLS params.

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

IDL11 (°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)
18.4876-2.1684-3.63838.5055-3.34518.73340.2471-0.89630.60.43730.1370.4536-0.61470.4713-0.25930.8213-0.2063-0.21251.0516-0.22791.437-97.548628.72515.1443
22.13040.732-0.13874.46620.6261-0.18790.3095-0.68271.8511.22230.14733.2837-0.03650.0943-0.21961.3587-0.29750.01881.19970.23682.1851-109.432818.7506-4.824
32.44611.1176-2.10434.6389-1.01783.3921-0.28640.21540.0928-0.32520.10790.2480.27760.04510.16011.0077-0.2218-0.35371.02210.22021.0728-100.3987-0.8577-18.2839
44.5522-4.2928-4.70034.49084.66447.01310.50481.089-1.026-1.46590.49230.8998-1.2050.4348-0.79081.6085-0.2117-0.12591.02330.3212.0583-97.488741.8541-24.3946
53.94584.7421-0.42076.14591.94739.01030.5903-0.349-0.1456-0.7783-0.1456-0.02730.00620.3872-0.81031.0841-0.3015-0.45931.16220.21951.9952-94.89229.6087-22.1321
62.86323.0296-0.30745.33980.0942.6770.1432-0.0141.192-0.01360.591.6571-0.4295-0.168-0.37791.0427-0.2388-0.2581.09120.01621.8974-103.293635.1643-14.3403
73.62280.2918-0.86562.808-0.04233.8959-0.3092-0.49720.26730.22060.1434-1.0071-0.31180.73230.36570.8681-0.1147-0.24211.5778-0.07641.4928-73.511117.7042-5.938
82.0572-0.628-1.74982.50591.0442.754-0.2776-0.8925-0.2762-0.04190.4942-0.3660.50040.8747-0.41190.73980.0431-0.25741.542-0.17251.2735-68.60068.1199-0.5686
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 113 )
2X-RAY DIFFRACTION2chain 'A' and (resid 114 through 164 )
3X-RAY DIFFRACTION3chain 'A' and (resid 165 through 382 )
4X-RAY DIFFRACTION4chain 'D' and (resid 7 through 42 )
5X-RAY DIFFRACTION5chain 'D' and (resid 43 through 83 )
6X-RAY DIFFRACTION6chain 'D' and (resid 84 through 133 )
7X-RAY DIFFRACTION7chain 'D' and (resid 134 through 207 )
8X-RAY DIFFRACTION8chain 'D' and (resid 208 through 382 )

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