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- PDB-8dvq: CA domain of VanSA histidine kinase -

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Basic information

Entry
Database: PDB / ID: 8dvq
TitleCA domain of VanSA histidine kinase
ComponentsSensor protein VanS
KeywordsSIGNALING PROTEIN / ATP-binding / histidine kinase
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / cell wall organization / negative regulation of DNA-binding transcription factor activity / response to antibiotic / ATP binding / plasma membrane
Similarity search - Function
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 / Signal transduction histidine kinase-related protein, C-terminal / 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
: / Sensor protein VanS
Similarity search - Component
Biological speciesEnterococcus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.19 Å
AuthorsLoll, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI148679 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Structure of VanS from vancomycin-resistant enterococci: A sensor kinase with weak ATP binding.
Authors: Grasty, K.C. / Guzik, C. / D'Lauro, E.J. / Padrick, S.B. / Beld, J. / Loll, P.J.
History
DepositionJul 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sensor protein VanS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4803
Polymers18,2561
Non-polymers2252
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.830, 94.400, 29.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab

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Components

#1: Protein Sensor protein VanS / / Vancomycin histidine protein kinase / Vancomycin resistance protein VanS


Mass: 18255.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus (bacteria) / Gene: vanS / Plasmid: pETHSUL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q06240, histidine kinase
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.69 Å3/Da / Density % sol: 54.23 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 8.2
Details: Protein and precipitant were mixed in a volume ratio of 1:2 and incubated under Als Oil at 291K; the precipitant solution was obtained from the Berkeley Screen and contained 75 mM Bis-Tris ...Details: Protein and precipitant were mixed in a volume ratio of 1:2 and incubated under Als Oil at 291K; the precipitant solution was obtained from the Berkeley Screen and contained 75 mM Bis-Tris Propane, 25 mM citric acid, pH 8.2, 20 mM CdCl2, and 25 (w-v) PEG 400.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92009 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92009 Å / Relative weight: 1
ReflectionResolution: 2.19→28.7 Å / Num. obs: 10676 / % possible obs: 99.7 % / Redundancy: 8.55 % / Biso Wilson estimate: 43.41 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.033 / Rrim(I) all: 0.096 / Net I/σ(I): 13
Reflection shellResolution: 2.19→2.27 Å / Num. unique obs: 1031 / CC1/2: 0.849 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHENIX1.14_3260phasing
RefinementMethod to determine structure: SAD / Resolution: 2.19→28.69 Å / SU ML: 0.1943 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.4862 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2362 533 5.02 %
Rwork0.1897 10088 -
obs0.192 10621 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63 Å2
Refinement stepCycle: LAST / Resolution: 2.19→28.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1015 0 2 45 1062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01141033
X-RAY DIFFRACTIONf_angle_d1.26131400
X-RAY DIFFRACTIONf_chiral_restr0.0721162
X-RAY DIFFRACTIONf_plane_restr0.0062181
X-RAY DIFFRACTIONf_dihedral_angle_d3.7566619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.410.29161300.23952450X-RAY DIFFRACTION99.04
2.41-2.760.29741330.20572481X-RAY DIFFRACTION99.77
2.76-3.480.251330.21972502X-RAY DIFFRACTION99.55
3.48-28.690.21221370.16712655X-RAY DIFFRACTION99.57
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)
14.83124152728-0.374872421975-2.17112189312.471500532210.4904284635744.66301367010.0657759289103-0.084039209912-0.155006149106-0.04223041629710.08645781531090.06960610348290.097820319406-0.0142221317141-0.1051029545340.2715414821070.00323465745488-0.04721142304710.450490206737-0.0148034339680.27324043270840.68615.13812.781
24.33811096664E-1102.2299911772E-133.75814505167E-1203.84115306345E-113596.37996069-152660.128719-1399242.78689-8.3018064856E-8-4.97755578484E-7-60608.838681117733.04478-35129.2758823-3596.379960190.525155533325-0.0829376151293-0.01021163275930.9827494926330.1229603759110.56599637925257.86524.6168.917
39.16732247575E-11-6.47466404143E-12-6.47466404073E-127.74874509637E-117.12088632253E-117.12088632253E-11104419.0320071920241.006521036647.35999-1733725.30126-146335.46053541916.4285225-1531211.61103-146335.46052341916.42852750.7001333783080.0930235634667-0.05188703866340.792400289519-0.02281897180150.49320841248746.8820.16526.074
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 9:157 )A9 - 157
2X-RAY DIFFRACTION2( CHAIN A AND RESID 201:201 )A201
3X-RAY DIFFRACTION3( CHAIN A AND RESID 202:202 )A202

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