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- PDB-5gpo: The sensor domain structure of the zinc-responsive histidine kina... -

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Basic information

Entry
Database: PDB / ID: 5gpo
TitleThe sensor domain structure of the zinc-responsive histidine kinase CzcS from Pseudomonas Aeruginosa
ComponentsSensor protein CzcS
KeywordsTRANSFERASE / two-component system / heavy metals / histidine kinase
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / membrane => GO:0016020 / ATP binding / plasma membrane
Similarity search - Function
Heavy metal sensor kinase / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP 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 / Signal transduction histidine kinase-related protein, C-terminal ...Heavy metal sensor kinase / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP 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 / 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 / Sensor protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.701 Å
AuthorsWang, D. / Chen, W.Z. / Huang, S.Q. / Liu, X.C. / Hu, Q.Y. / Wei, T.B. / Gan, J.H. / Chen, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of ChinaNSFC, 20721002 China
CitationJournal: PLoS Pathog. / Year: 2017
Title: Structural basis of Zn(II) induced metal detoxification and antibiotic resistance by histidine kinase CzcS in Pseudomonas aeruginosa
Authors: Wang, D. / Chen, W. / Huang, S. / He, Y. / Liu, X. / Hu, Q. / Wei, T. / Shang, H. / Gan, J. / Chen, H.
History
DepositionAug 3, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 20, 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
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_asym_id / _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.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sensor protein CzcS
B: Sensor protein CzcS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3578
Polymers28,8422
Non-polymers5156
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-45 kcal/mol
Surface area12260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.337, 47.705, 57.528
Angle α, β, γ (deg.)90.00, 91.63, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-201-

ZN

21B-202-

SO4

31A-413-

HOH

41A-426-

HOH

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Components

#1: Protein Sensor protein CzcS /


Mass: 14421.085 Da / Num. of mol.: 2 / Fragment: UNP residues 40-165
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: czcS_3, AOY09_03645 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3
References: UniProt: A0A0C7CWG4, UniProt: Q9I0V9*PLUS, histidine kinase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.16 Å3/Da / Density % sol: 42.97 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: Ammonium sulfate, Bis-tris, PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 26314 / % possible obs: 94.5 % / Redundancy: 5.2 % / Rsym value: 0.067 / Net I/σ(I): 21.8
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.2 / % possible all: 92.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.701→28.752 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 26.8
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2532 1318 5.01 %
Rwork0.2102 --
obs0.2124 26314 94.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.701→28.752 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1841 0 22 233 2096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071901
X-RAY DIFFRACTIONf_angle_d0.8342579
X-RAY DIFFRACTIONf_dihedral_angle_d14.6541187
X-RAY DIFFRACTIONf_chiral_restr0.048299
X-RAY DIFFRACTIONf_plane_restr0.006341
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7005-1.76860.29691250.24832639X-RAY DIFFRACTION91
1.7686-1.84910.27821680.24032663X-RAY DIFFRACTION92
1.8491-1.94650.38861340.30962587X-RAY DIFFRACTION88
1.9465-2.06840.32841540.25232741X-RAY DIFFRACTION94
2.0684-2.22810.29031360.23722810X-RAY DIFFRACTION95
2.2281-2.45220.24961300.24552808X-RAY DIFFRACTION94
2.4522-2.80680.22441640.20862898X-RAY DIFFRACTION98
2.8068-3.53520.24181490.19472865X-RAY DIFFRACTION97
3.5352-28.75650.22351580.17322985X-RAY DIFFRACTION98

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