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- PDB-4ywz: Crystal structure of the extracellular receptor domain of the ess... -

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Basic information

Entry
Database: PDB / ID: 4ywz
TitleCrystal structure of the extracellular receptor domain of the essential sensor kinase WalK from Staphylococcus aureus
ComponentsSensor protein kinase WalK
KeywordsTRANSFERASE / extracellular receptor / kinase / essential / staphylococcus aureus
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / membrane => GO:0016020 / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
Periplasmic sensor-like domain superfamily / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / PAS-associated, C-terminal / PAC domain profile. / PAS domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain ...Periplasmic sensor-like domain superfamily / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / PAS-associated, C-terminal / PAC domain profile. / PAS domain / 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 / PAS domain / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Beta-Lactamase / PAS domain / PAS repeat profile. / PAS domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Sensor protein kinase WalK / Sensor protein kinase WalK
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsJi, Q. / Wawrzak, Z. / He, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI074658 United States
CitationJournal: Nat Commun / Year: 2016
Title: Structure and mechanism of the essential two-component signal-transduction system WalKR in Staphylococcus aureus.
Authors: Ji, Q. / Chen, P.J. / Qin, G. / Deng, X. / Hao, Z. / Wawrzak, Z. / Yeo, W.S. / Quang, J.W. / Cho, H. / Luo, G.Z. / Weng, X. / You, Q. / Luan, C.H. / Yang, X. / Bae, T. / Yu, K. / Jiang, H. / He, C.
History
DepositionMar 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sensor protein kinase WalK
B: Sensor protein kinase WalK


Theoretical massNumber of molelcules
Total (without water)34,8032
Polymers34,8032
Non-polymers00
Water6,954386
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Sensor protein kinase WalK


Theoretical massNumber of molelcules
Total (without water)17,4011
Polymers17,4011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Sensor protein kinase WalK


Theoretical massNumber of molelcules
Total (without water)17,4011
Polymers17,4011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.701, 66.701, 80.492
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Sensor protein kinase WalK /


Mass: 17401.359 Da / Num. of mol.: 2
Fragment: extracellular receptor domain (UNP residues 34-182)
Mutation: A86M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: walK, yycG, SAB0019 / Production host: Escherichia coli (E. coli)
References: UniProt: Q2YUQ2, UniProt: A6QD58*PLUS, histidine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2.97 Å3/Da / Density % sol: 58.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.1
Details: 0.2 M ammonium citrate dibasic, 20% w/v polyethylene glycol 3350, pH 5.1

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 44089 / % possible obs: 100 % / Redundancy: 5.7 % / Net I/σ(I): 41.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RESOLVEphasing
RefinementResolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.85 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19667 2124 4.8 %RANDOM
Rwork0.1648 ---
obs0.16632 41930 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.709 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.05 Å2-0 Å2
2--0.1 Å20 Å2
3----0.31 Å2
Refinement stepCycle: 1 / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2364 0 0 386 2750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.022387
X-RAY DIFFRACTIONr_bond_other_d0.0010.022366
X-RAY DIFFRACTIONr_angle_refined_deg2.2051.963208
X-RAY DIFFRACTIONr_angle_other_deg0.97235444
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1435290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.50827.28125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.86415479
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.844156
X-RAY DIFFRACTIONr_chiral_restr0.1380.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022736
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02522
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.882.5731169
X-RAY DIFFRACTIONr_mcbond_other2.8672.5711168
X-RAY DIFFRACTIONr_mcangle_it4.1073.8421456
X-RAY DIFFRACTIONr_mcangle_other4.1073.8431457
X-RAY DIFFRACTIONr_scbond_it4.7523.1431218
X-RAY DIFFRACTIONr_scbond_other4.753.1441219
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9534.4651753
X-RAY DIFFRACTIONr_long_range_B_refined9.01323.4153100
X-RAY DIFFRACTIONr_long_range_B_other8.62921.6562836
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 106 -
Rwork0.228 3151 -
obs--98.91 %

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