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- PDB-7v4e: Crystal Structure of VpsR display novel dimeric architecture and ... -

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Basic information

Entry
Database: PDB / ID: 7v4e
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
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 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 12, 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

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Assembly

Deposited unit
A: VpsR
D: VpsR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,0176
Polymers89,4442
Non-polymers1,5734
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, SEC and DLS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-58 kcal/mol
Surface area39110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.687, 119.687, 81.141
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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9AQ41
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate


Mass: 690.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O14P2 / Feature type: SUBJECT OF INVESTIGATION
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: 3.75 Å3/Da / Density % sol: 67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.8M AMS, Bicine pH 8.8, NaCl 300mM / 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: 0.974 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 27, 2021 / Details: bent cylindrical
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.974 Å / Relative weight: 1
ReflectionResolution: 4→48.162 Å / Num. obs: 19802 / % possible obs: 95 % / Redundancy: 3.3 % / CC1/2: 0.95 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.063 / Rrim(I) all: 0.127 / Net I/σ(I): 9.2
Reflection shellResolution: 4→4.14 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.342 / Num. unique obs: 1095 / CC1/2: 0.86 / Rpim(I) all: 0.211 / Rrim(I) all: 0.405 / % possible all: 99.2

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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: 4→48.162 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 0.22 / Phase error: 34.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2797 1992 10.06 %
Rwork0.2415 --
obs0.2452 19802 90.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4→48.162 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5872 0 102 0 5974
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036092
X-RAY DIFFRACTIONf_angle_d0.9538270
X-RAY DIFFRACTIONf_dihedral_angle_d17.2022244
X-RAY DIFFRACTIONf_chiral_restr0.033942
X-RAY DIFFRACTIONf_plane_restr0.0041050
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.0001-4.10010.3721500.3411268X-RAY DIFFRACTION93
4.1001-4.21090.38851550.32631300X-RAY DIFFRACTION93
4.2109-4.33470.34491360.30731300X-RAY DIFFRACTION91
4.3347-4.47460.30591470.28961246X-RAY DIFFRACTION88
4.4746-4.63440.33691310.26011252X-RAY DIFFRACTION89
4.6344-4.81980.36231540.2821268X-RAY DIFFRACTION88
4.8198-5.03890.29061420.26011287X-RAY DIFFRACTION94
5.0389-5.30420.36211480.27761301X-RAY DIFFRACTION93
5.3042-5.63610.2951430.28211287X-RAY DIFFRACTION91
5.6361-6.07050.36161530.28291219X-RAY DIFFRACTION87
6.0705-6.680.31441370.27861273X-RAY DIFFRACTION89
6.68-7.64320.271290.24371306X-RAY DIFFRACTION93
7.6432-9.61710.21171410.20241232X-RAY DIFFRACTION86
9.6171-48.1620.22091260.18971271X-RAY DIFFRACTION90

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