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- PDB-7cus: Crystal structure of the sensor domain of VbrK from Vibrio paraha... -

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Basic information

Entry
Database: PDB / ID: 7cus
TitleCrystal structure of the sensor domain of VbrK from Vibrio parahaemolyticus
ComponentsDUF3404 domain-containing protein
KeywordsSIGNALING PROTEIN / sensor domain / beta-lactam antibiotic receptor
Function / homology
Function and homology information


phosphorelay sensor kinase activity / membrane => GO:0016020
Similarity search - Function
Protein of unknown function DUF3404 / Domain of unknown function (DUF3404) / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases ...Protein of unknown function DUF3404 / Domain of unknown function (DUF3404) / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
DUF3404 domain-containing protein / Sensor histidine kinase
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsCho, S.Y. / Yoon, S.I.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Structural analysis of the sensor domain of the beta-lactam antibiotic receptor VbrK from Vibrio parahaemolyticus.
Authors: Cho, S.Y. / Yoon, S.I.
History
DepositionAug 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DUF3404 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)25,1721
Polymers25,1721
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11590 Å2
Unit cell
Length a, b, c (Å)29.686, 69.875, 106.498
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein DUF3404 domain-containing protein / Histidine kinase


Mass: 25171.549 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria)
Gene: C1S91_03980, CGH73_12765, CGI34_20575, CGI42_14745, E4P16_22270, F0L89_03255
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0F2H8K1, UniProt: Q87HP3*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

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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: 2.19 Å3/Da / Density % sol: 43.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, di-ammonium hydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 27602 / % possible obs: 99.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 18.79 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 22
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1334 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R7Q

4r7q


Resolution: 1.65→29.21 Å / SU ML: 0.1482 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.2476
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2086 1398 5.09 %
Rwork0.1819 26052 -
obs0.1833 26052 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.2 Å2
Refinement stepCycle: LAST / Resolution: 1.65→29.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1703 0 0 150 1853
LS refinement shellResolution: 1.65→1.709 Å
RfactorNum. reflection% reflection
Rfree0.2476 122 -
Rwork0.2054 2532 -
obs--100 %
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)
10.681085947088-0.318127134197-1.351567176670.1817616192890.3884234468293.8763428417-0.07000023635870.090512364537-0.0490211554203-0.02146149067080.01443593945540.076968805150.0539179533753-0.2076934953980.05832250932140.165495889674-0.0323983464959-3.87286535982E-50.1853471203920.01130893223710.179344221679-6.88894218632-3.957151883426.812096897
21.76313063109-0.288877718314-0.9268633928772.23857246959-0.1653550991932.591231175470.120382816845-0.1271421309730.009670733294450.0604900677183-0.118705243433-0.0500422739611-0.10010951740.125470387271-0.02005865707890.0693871585181-0.0124099425315-0.009761297182620.1316239500940.008996934030550.1192249653855.25155945632-2.285179984485.05424292163
31.857775140850.675124652217-0.5140088435372.560348651950.4685440290113.32584253259-0.1230613037360.00353612024507-0.1455219820680.02518083658750.0737869253364-0.002104825562650.284638219449-0.05503166426750.02518287741140.1087492844270.01191063220180.007404392065130.1081028151480.02062597630950.125338802601-5.83186992195-7.9423873538236.9206279944
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 72 )
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 170 )
3X-RAY DIFFRACTION3chain 'A' and (resid 171 through 238 )

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