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- PDB-7v3w: Crystal Structure of VpsR display novel dimeric architecture and ... -

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Basic information

Entry
Database: PDB / ID: 7v3w
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
ADENOSINE-5'-TRIPHOSPHATE / VpsR
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.205 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 11, 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)90,4594
Polymers89,4442
Non-polymers1,0142
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, SEC, DLS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-34 kcal/mol
Surface area37040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.788, 118.788, 79.146
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-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestN

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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: 3.6 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting 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: 0.987 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: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.2→47.51 Å / Num. obs: 20013 / % possible obs: 97.6 % / Redundancy: 2.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.042 / Rrim(I) all: 0.077 / Net I/σ(I): 11.9
Reflection shellResolution: 3.2→3.43 Å / Rmerge(I) obs: 1.373 / Num. unique obs: 1896 / CC1/2: 0.363 / Rpim(I) all: 0.894 / Rrim(I) all: 1.651 / % possible all: 98.7

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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: 3.205→47.505 Å / Cross valid method: FREE R-VALUE / σ(F): 0.29 / Phase error: 34.93 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2732 1922 4.92 %
Rwork0.224 --
obs0.2315 20013 95.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.205→47.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5882 0 62 0 5944
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036056
X-RAY DIFFRACTIONf_angle_d0.9428212
X-RAY DIFFRACTIONf_dihedral_angle_d16.9722270
X-RAY DIFFRACTIONf_chiral_restr0.034936
X-RAY DIFFRACTIONf_plane_restr0.0041050
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2085-3.28860.48021500.43382740X-RAY DIFFRACTION93
3.2886-3.37740.36791480.42562744X-RAY DIFFRACTION94
3.3774-3.47670.37681400.37132736X-RAY DIFFRACTION93
3.4767-3.58880.34851140.36542692X-RAY DIFFRACTION94
3.5888-3.71680.31011500.3482714X-RAY DIFFRACTION92
3.7168-3.86540.29461400.32712714X-RAY DIFFRACTION92
3.8654-4.0410.32471360.32992734X-RAY DIFFRACTION94
4.041-4.25350.2651480.29152712X-RAY DIFFRACTION93
4.2535-4.51930.28221400.26712590X-RAY DIFFRACTION91
4.5193-4.86710.2871300.24682688X-RAY DIFFRACTION91
4.8671-5.35470.22411360.22472670X-RAY DIFFRACTION91
5.3547-6.12460.27921340.24762568X-RAY DIFFRACTION88
6.1246-7.69760.33051280.22042466X-RAY DIFFRACTION85
7.6976-31.46630.2291280.12692347X-RAY DIFFRACTION80
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)
12.91816.3972-5.71324.91110.82555.8844-0.4979-1.6216-0.32861.7526-1.468-0.7367-0.4419-0.27741.06871.62530.15340.02631.66970.03381.108578.46143.94799.7476
24.50063.41010.5417.5967.04321.4202-0.34590.298-0.36550.15050.4155-0.75190.60470.0806-0.14591.54610.03840.16391.52210.1520.940373.7292137.24570.9344
38.9097-7.82013.18611.4973-0.61546.9804-0.1634-1.185-1.38491.7287-0.6960.5351-1.9168-0.6070.50451.8345-0.09320.28221.47580.01711.756667.1009161.2423-6.3787
43.41845.23090.01937.8578-2.29088.7645-0.9127-2.5772-2.76662.0048-0.7892-2.6690.69790.39951.39632.15570.0194-0.52751.54090.24750.874961.7267153.2471-11.2442
51.7839-1.07451.52345.361-2.75132.92230.27261.0194-0.0456-1.8761-0.0904-0.2446-0.71710.1764-0.15182.30030.21440.41851.66440.09150.831453.5607150.7286-29.8015
63.2617-3.8621-3.84371.04261.8216-0.129-0.38240.3746-0.2447-0.1687-1.05630.3291.17060.24271.31062.07550.1560.26021.7020.09021.055150.7922155.8697-11.9138
78.25350.801-0.316110.192-3.72011.10950.0173-1.7116-0.06840.14920.23290.39040.12950.29850.11821.6532-0.02020.00231.6483-0.11010.717437.4403168.6366-3.5551
89.3437-3.37361.90762.90894.98226.31540.06141.6687-0.2567-1.0087-0.3429-0.38990.29031.16340.19711.7329-0.17960.40921.96030.02091.424482.4324131.0278-25.8826
911.24911.62030.07123.998-1.7394.04720.88070.05730.4782-1.3827-2.4547-1.5685-0.3620.49471.30071.93920.38960.32321.98670.34231.097373.689138.1599-21.7719
102.8051-4.43150.56548.7379-1.23169.3305-0.86781.968-1.18682.83840.62470.5689-0.418-1.03680.35392.38690.18960.30611.5844-0.02711.008381.8445146.8245-17.8234
114.37640.6521.11913.0225-1.1120.63810.4813-0.2559-0.7460.2928-0.21410.06640.9719-0.4039-0.21092.4182-0.1343-0.03741.77440.0390.622255.9384124.9647-2.3246
1210.2266-4.0453-4.630410.43694.49474.36090.39681.35811.90763.9782-2.54975.83882.9304-2.196-0.38842.5407-0.5158-0.20171.66911.77020.803848.1724127.62347.7736
135.22320.91950.75562.951.72890.18230.55010.79710.2309-0.06090.26550.2010.2749-0.1957-0.76131.7472-0.0767-0.23871.33750.30191.035239.8462123.4219-5.8005
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 42 )
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 128 )
3X-RAY DIFFRACTION3chain 'A' and (resid 129 through 151 )
4X-RAY DIFFRACTION4chain 'A' and (resid 152 through 174 )
5X-RAY DIFFRACTION5chain 'A' and (resid 175 through 289 )
6X-RAY DIFFRACTION6chain 'A' and (resid 290 through 332 )
7X-RAY DIFFRACTION7chain 'A' and (resid 333 through 382 )
8X-RAY DIFFRACTION8chain 'D' and (resid 7 through 51 )
9X-RAY DIFFRACTION9chain 'D' and (resid 52 through 86 )
10X-RAY DIFFRACTION10chain 'D' and (resid 87 through 115 )
11X-RAY DIFFRACTION11chain 'D' and (resid 116 through 227 )
12X-RAY DIFFRACTION12chain 'D' and (resid 228 through 246 )
13X-RAY DIFFRACTION13chain 'D' and (resid 247 through 382 )

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