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- PDB-7v2v: Crystal Structure of VpsR display novel dimeric architecture and ... -

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Basic information

Entry
Database: PDB / ID: 7v2v
TitleCrystal Structure of VpsR display novel dimeric architecture and c-di-GMP binding: mechanistic implications in oligomerization, ATPase activity and DNA binding.
ComponentsVpsR
KeywordsTRANSCRIPTION / 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: 3.194 Å
AuthorsChakrabortty, T. / Sen, U. / Chowdhury, S.R.
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 10, 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)89,6364
Polymers89,4442
Non-polymers1922
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, SEC and DLS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-70 kcal/mol
Surface area37870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.921, 119.921, 81.601
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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / 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: 3.79 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: AMS bicine pH 8.8 300 NaCl / 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: 0.9724 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: 0.9724 Å / Relative weight: 1
ReflectionResolution: 3.19→48.4 Å / Num. obs: 21513 / % possible obs: 98.2 % / Redundancy: 3.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.059 / Rrim(I) all: 0.121 / Net I/σ(I): 6.8
Reflection shellResolution: 3.19→3.31 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.123 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2212 / CC1/2: 0.314 / Rpim(I) all: 0.697 / Rrim(I) all: 1.33 / % possible all: 99.3

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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: 3.194→48.319 Å / Cross valid method: FREE R-VALUE / Phase error: 36.44 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.269 3686 9.4 %
Rwork0.2338 --
obs0.2395 21412 89.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.194→48.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5872 0 10 0 5882
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045988
X-RAY DIFFRACTIONf_angle_d0.8798106
X-RAY DIFFRACTIONf_dihedral_angle_d14.9412236
X-RAY DIFFRACTIONf_chiral_restr0.031926
X-RAY DIFFRACTIONf_plane_restr0.0041046
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.198-3.25310.39951900.43061802X-RAY DIFFRACTION81
3.2531-3.31230.43181980.40921724X-RAY DIFFRACTION81
3.3123-3.37590.37331920.39931843X-RAY DIFFRACTION82
3.3759-3.44480.36661760.38211710X-RAY DIFFRACTION81
3.4448-3.51970.33781760.34951814X-RAY DIFFRACTION82
3.5197-3.60150.37281880.36731741X-RAY DIFFRACTION81
3.6015-3.69160.34251720.34681758X-RAY DIFFRACTION82
3.6916-3.79130.38041880.32591767X-RAY DIFFRACTION82
3.7913-3.90280.32572140.33331778X-RAY DIFFRACTION81
3.9028-4.02870.28951560.3181769X-RAY DIFFRACTION83
4.0287-4.17260.31461760.29931750X-RAY DIFFRACTION82
4.1726-4.33950.34291880.27761777X-RAY DIFFRACTION81
4.3395-4.53680.31451780.25161810X-RAY DIFFRACTION81
4.5368-4.77570.27271940.26141734X-RAY DIFFRACTION81
4.7757-5.07450.2251860.23981762X-RAY DIFFRACTION81
5.0745-5.46570.29151900.24591765X-RAY DIFFRACTION81
5.4657-6.01440.30051800.27971821X-RAY DIFFRACTION83
6.0144-6.88190.34041820.23841783X-RAY DIFFRACTION83
6.8819-8.65940.21791780.18571775X-RAY DIFFRACTION82
8.6594-43.81330.20051840.141816X-RAY DIFFRACTION83
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)
19.5003-1.1699-1.64619.4415-1.43675.72790.69380.94350.5253-0.2846-0.2360.7560.4353-0.9798-0.67741.1472-0.06280.06251.2280.03330.9413-75.861141.7261-1.619
26.07492.4633-0.44218.8874-0.68134.27030.12180.07960.08930.09230.20780.50960.20470.1598-0.33041.19530.01090.08940.9139-0.12460.6075-52.0102157.513319.7915
38.58271.21991.74652.0462-0.18846.50770.6804-0.36230.50550.2925-0.22620.914-0.4388-0.8191-0.46961.6584-0.08430.23551.45340.03081.2938-79.3237135.519825.2481
47.8225-3.8534-0.1185.85510.68623.22620.6347-0.361-1.5705-2.2574-0.18740.9480.3305-0.3372-0.26361.7668-0.19410.01711.25910.18021.243-76.2469135.364315.8902
53.9964-0.92690.71176.2729-0.43610.14350.2409-0.0276-0.1893-0.0080.1552-0.1969-0.36840.4149-0.38411.50930.19990.02991.1945-0.22410.6308-44.3774125.63722.7729
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 134 )
2X-RAY DIFFRACTION2chain 'A' and (resid 135 through 382 )
3X-RAY DIFFRACTION3chain 'D' and (resid 9 through 87 )
4X-RAY DIFFRACTION4chain 'D' and (resid 88 through 151 )
5X-RAY DIFFRACTION5chain 'D' and (resid 152 through 382 )

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