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- PDB-7y19: Transcriptional regulator BrpR -

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Basic information

Entry
Database: PDB / ID: 7y19
TitleTranscriptional regulator BrpR
ComponentsTranscriptional regulator VpsR
KeywordsTRANSCRIPTION / Vibrio vulnificus / biofilm / colony morphology / transcriptional regulator
Function / homology
Function and homology information


sequence-specific DNA binding / regulation of DNA-templated transcription / ATP binding
Similarity search - Function
VpsR domain / VpsR domain / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / 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 ...VpsR domain / VpsR domain / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / 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
Transcriptional regulator VpsR
Similarity search - Component
Biological speciesVibrio vulnificus CMCP6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.39 Å
AuthorsKi, N. / Ha, N.C. / Seung-Ho, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural basis for the biofilm regulation of transcription factor BrpR in Vibrio vulnificus
Authors: Ki, N. / Seung-Ho, H.
History
DepositionJun 7, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator VpsR


Theoretical massNumber of molelcules
Total (without water)16,3211
Polymers16,3211
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.259, 53.259, 143.926
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Transcriptional regulator VpsR / transcriptional regulator BrpR


Mass: 16321.154 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus CMCP6 (bacteria) / Strain: CMCP6 / Gene: VV1_0525 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3Q0L274
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
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: 1.83 Å3/Da / Density % sol: 32.65 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop
Details: 0.035 M Citric acid, 0.065 M BIS-TRIS propane pH 7.0, 22% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.0448 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0448 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 5217 / % possible obs: 98.6 % / Redundancy: 24.2 % / Biso Wilson estimate: 29.48 Å2 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.019 / Rrim(I) all: 0.107 / Χ2: 1.129 / Net I/σ(I): 17.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.4412.80.3092520.9480.0820.3210.86296.9
2.44-2.4914.80.3032360.9250.0750.3130.86397.9
2.49-2.5315.30.2982520.9390.0730.3070.82599.2
2.53-2.59160.2882420.9440.0680.2960.91897.2
2.59-2.6418.50.2652480.9750.0590.2720.9398.4
2.64-2.718.30.2452520.9850.0530.2511.06198.8
2.7-2.7718.80.2572520.9750.0560.2631.03898.4
2.77-2.8521.10.2232540.9950.0460.2281.11499.6
2.85-2.93210.2182510.9910.0450.2231.1399.2
2.93-3.0221.40.1922530.9910.040.1961.19498.4
3.02-3.1322.10.1812610.9950.0370.1851.20299.2
3.13-3.26260.1682500.9950.0310.1711.40199.6
3.26-3.4128.80.1612620.9960.0290.1641.40698.9
3.41-3.5831.50.1472670.9980.0250.1491.4699.6
3.58-3.8133.40.1432670.9980.0240.1451.47198.9
3.81-4.133.70.1262610.9960.0210.1281.39499.6
4.1-4.5233.80.1062710.9990.0180.1081.13898.9
4.52-5.1732.20.12760.9910.0170.1011.0699.3
5.17-6.51280.0912840.9990.0170.0920.86799
6.51-5029.90.0663260.9990.0120.0670.63195.9

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.39→33.25 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 2.52 / Phase error: 23.63 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2908 520 10 %
Rwork0.2206 4679 -
obs0.2275 5199 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.79 Å2 / Biso mean: 31.4427 Å2 / Biso min: 7.27 Å2
Refinement stepCycle: final / Resolution: 2.39→33.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1035 0 0 4 1039
Biso mean---15.59 -
Num. residues----132
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.39-2.630.31031210.23581093121496
2.63-3.010.30291260.2481139126599
3.02-3.80.29081320.2211741306100
3.8-33.250.27941410.206512731414100

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