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- PDB-8dwz: CA domain of VanSA histidine kinase, 7 keV data -

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Basic information

Entry
Database: PDB / ID: 8dwz
TitleCA domain of VanSA histidine kinase, 7 keV data
ComponentsSensor protein VanS
KeywordsSIGNALING PROTEIN / ATP-binding / histidine kinase
Function / homology
Function and homology information


cellular response to phosphate starvation / phosphorelay sensor kinase activity / histidine kinase / phosphoprotein phosphatase activity / negative regulation of DNA-binding transcription factor activity / cell wall organization / 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-related protein, C-terminal / 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 superfamily
Similarity search - Domain/homology
: / Sensor protein VanS
Similarity search - Component
Biological speciesEnterococcus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.21 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
DepositionAug 2, 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
Water43224
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
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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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 / 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


Mass: 18.015 Da / Num. of mol.: 24 / 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: VanSA CA domain protein was at a concentration of 2.5 mg/mL in 20 mM Tris pH 7.8, 150 mM NaCl, supplemented with 2.5 mM AMP-PNP and 5 mM MgCl2. Protein and precipitant were mixed in a volume ...Details: VanSA CA domain protein was at a concentration of 2.5 mg/mL in 20 mM Tris pH 7.8, 150 mM NaCl, supplemented with 2.5 mM AMP-PNP and 5 mM MgCl2. Protein and precipitant were mixed in a volume ratio of 1:2 and incubated under Als Oil at 291 K; the precipitant solution 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: APS / Beamline: 24-ID-C / Wavelength: 1.7712 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 2.21→56.14 Å / Num. obs: 17544 / % possible obs: 92.8 % / Redundancy: 18.4 % / Biso Wilson estimate: 39.78 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.023 / Rrim(I) all: 0.104 / Net I/σ(I): 23.1
Reflection shellResolution: 2.21→2.33 Å / Rmerge(I) obs: 0.578 / Num. unique obs: 1807 / CC1/2: 0.932 / Rpim(I) all: 0.206 / Rrim(I) all: 0.616

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.21→56.14 Å / SU ML: 0.2878 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 28.5489 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2325 911 5.19 %
Rwork0.1836 16633 -
obs0.1862 17544 92.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.65 Å2
Refinement stepCycle: LAST / Resolution: 2.21→56.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1006 0 2 24 1032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00651024
X-RAY DIFFRACTIONf_angle_d0.79341389
X-RAY DIFFRACTIONf_chiral_restr0.0582161
X-RAY DIFFRACTIONf_plane_restr0.0046180
X-RAY DIFFRACTIONf_dihedral_angle_d3.1833612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.330.3471980.26851709X-RAY DIFFRACTION66.56
2.33-2.480.29541490.22032415X-RAY DIFFRACTION93.37
2.48-2.670.28811250.20752441X-RAY DIFFRACTION95.78
2.67-2.940.24891370.19882497X-RAY DIFFRACTION97.05
2.94-3.360.27381280.19692511X-RAY DIFFRACTION97.63
3.36-4.240.21011370.18192535X-RAY DIFFRACTION98.56
4.24-56.140.19661370.15412525X-RAY DIFFRACTION98.85
Refinement TLS params.Method: refined / Origin x: 40.608 Å / Origin y: 15.229 Å / Origin z: 12.985 Å
111213212223313233
T0.3411306449 Å20.0013313942358 Å2-0.0199095205755 Å2-0.38325638024 Å20.0139395335933 Å2--0.320245495568 Å2
L5.34106411716 °2-0.0419164187245 °2-1.30726537918 °2-1.22005412971 °20.0165621685174 °2--4.79555162707 °2
S-0.0150904188999 Å °0.0777148223114 Å °-0.213487922446 Å °0.0267950904859 Å °0.055154728336 Å °0.0529205683076 Å °0.157047141432 Å °-0.0868618510402 Å °-0.0360700344974 Å °
Refinement TLS groupSelection details: ( CHAIN A AND RESID 228:375 )

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