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- PDB-4gt8: Crystal Structure of the Catalytic and ATP-binding Domain from Vr... -

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Basic information

Entry
Database: PDB / ID: 4gt8
TitleCrystal Structure of the Catalytic and ATP-binding Domain from VraS in Complex with ADP
ComponentsSensor protein vraS
KeywordsTRANSFERASE / Histidine kinase / ATP hydrolysis / Two-component system / Bacterial signalling / Kinase / ATP-binding / Phosphorylation / Membrane
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / membrane => GO:0016020 / protein dimerization activity / ATP binding / plasma membrane
Similarity search - Function
Sensor histidine kinase LiaS/VraS / Signal transduction histidine kinase, subgroup 3, dimerisation and phosphoacceptor domain / Histidine kinase / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Sensor protein VraS
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.51 Å
AuthorsLeonard, P.G. / Valverde, J. / Stock, A.M.
CitationJournal: To be Published
Title: Structure of the Staphylococcus aureus VraS Catalytic and ATP-binding Domain
Authors: Leonard, P.G. / Valverde, J. / Stock, A.M.
History
DepositionAug 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sensor protein vraS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2283
Polymers15,7771
Non-polymers4522
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.192, 47.233, 89.398
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sensor protein vraS


Mass: 15776.990 Da / Num. of mol.: 1 / Fragment: Catalytic and ATP-binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / ATCC 700699 / Gene: SAV1885, vraS / Plasmid: P535 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) T1R / References: UniProt: Q7A2Q0, histidine kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.09 Å3/Da / Density % sol: 41.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 100 mM Tris-HCl, 450 mM MgCl2, 30% (w/v) PEG 3350, pH 8.5, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9181 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 5, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9181 Å / Relative weight: 1
ReflectionResolution: 1.51→30 Å / Num. all: 21323 / Num. obs: 21323 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.7 % / Rsym value: 0.115 / Χ2: 1.823 / Net I/σ(I): 5.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allΧ2% possible allRsym value
1.51-1.5411.2210531.41898.9
1.54-1.5611.92.310541.43698.9
1.56-1.5912.42.810121.46399.5
1.59-1.6312.83.310751.48898.3
1.63-1.6612.93.910301.54298.60.988
1.66-1.713.14.410361.51399.10.884
1.7-1.7412.95.410651.54898.80.745
1.74-1.79135.510211.58998.20.733
1.79-1.8412.8710561.66498.10.571
1.84-1.912.98.210291.708980.495
1.9-1.9712.811.610731.78598.70.351
1.97-2.0512.916.110411.90798.60.258
2.05-2.1412.717.610511.904990.226
2.14-2.2612.622.610781.94598.80.176
2.26-2.412.725.610592.014990.156
2.4-2.5812.630.910851.95399.50.128
2.58-2.8412.73910902.03699.70.103
2.84-3.2513.351.210902.061000.079
3.25-4.113.668.811242.43599.90.063
4.1-3012.471.512012.74299.30.062

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å29.45 Å
Translation2.5 Å29.45 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RESOLVEphasing
PHENIX1.8_1066refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→29.451 Å / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8179 / SU ML: 0.1 / σ(F): 0 / Phase error: 24.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.199 1005 5.07 %RANDOM
Rwork0.1832 ---
obs0.184 19830 92.08 %-
all-19830 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.12 Å2 / Biso mean: 28.0859 Å2 / Biso min: 15.88 Å2
Refinement stepCycle: LAST / Resolution: 1.51→29.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1056 0 28 136 1220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071136
X-RAY DIFFRACTIONf_angle_d1.2081546
X-RAY DIFFRACTIONf_chiral_restr0.072175
X-RAY DIFFRACTIONf_plane_restr0.004194
X-RAY DIFFRACTIONf_dihedral_angle_d14.913450
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.51-1.5880.32841270.28522319244681
1.588-1.68750.2371300.23982505263587
1.6875-1.81780.26571350.21532565270089
1.8178-2.00070.20931460.18592644279092
2.0007-2.29010.20581520.16732835298797
2.2901-2.88490.20241520.18222884303698
2.8849-29.45640.16571630.16613073323699

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