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- PDB-5ku5: Crystal Structure of CusS Sensor Domain with Silver Bound -

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Basic information

Entry
Database: PDB / ID: 5ku5
TitleCrystal Structure of CusS Sensor Domain with Silver Bound
ComponentsSensor kinase CusS
KeywordsTRANSFERASE / PDC fold / Histidine kinase / Silver binding / Metal efflux system
Function / homology
Function and homology information


cellular response to silver ion / peptidyl-histidine phosphorylation / protein histidine kinase activity / histidine kinase / phosphorelay signal transduction system / plasma membrane => GO:0005886 / phosphorelay sensor kinase activity / cellular response to copper ion / phosphorylation / signal transduction ...cellular response to silver ion / peptidyl-histidine phosphorylation / protein histidine kinase activity / histidine kinase / phosphorelay signal transduction system / plasma membrane => GO:0005886 / phosphorelay sensor kinase activity / cellular response to copper ion / phosphorylation / signal transduction / ATP binding / membrane / metal ion 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
ACETATE ION / SILVER ION / Sensor histidine kinase CusS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsAffandi, T. / Issaian, A.V. / McEvoy, M.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM079192 United States
CitationJournal: Biochemistry / Year: 2016
Title: The Structure of the Periplasmic Sensor Domain of the Histidine Kinase CusS Shows Unusual Metal Ion Coordination at the Dimeric Interface.
Authors: Affandi, T. / Issaian, A.V. / McEvoy, M.M.
History
DepositionJul 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sensor kinase CusS
B: Sensor kinase CusS
C: Sensor kinase CusS
D: Sensor kinase CusS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,40313
Polymers67,4814
Non-polymers9229
Water3,729207
1
A: Sensor kinase CusS
B: Sensor kinase CusS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1726
Polymers33,7402
Non-polymers4314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-20 kcal/mol
Surface area16580 Å2
MethodPISA
2
C: Sensor kinase CusS
D: Sensor kinase CusS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2317
Polymers33,7402
Non-polymers4915
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-18 kcal/mol
Surface area16370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.225, 96.289, 203.664
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein
Sensor kinase CusS


Mass: 16870.213 Da / Num. of mol.: 4 / Fragment: residues 39-187
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: cusS, ybcZ, b0570, JW5082 / Production host: Escherichia coli (E. coli) / References: UniProt: P77485, histidine kinase
#2: Chemical
ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ag
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.6 Å3/Da / Density % sol: 52.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 100 mM Tris HCl pH 8.5 200 mM Ammonium acetate 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.036 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.036 Å / Relative weight: 1
ReflectionResolution: 2.15→33.29 Å / Num. obs: 38599 / % possible obs: 99 % / Redundancy: 3.48 % / Net I/σ(I): 6.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→33.29 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.9 / SU B: 8.019 / SU ML: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.291 / ESU R Free: 0.229
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2864 1910 5 %RANDOM
Rwork0.2497 ---
obs0.2515 36652 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 70.05 Å2 / Biso mean: 34.471 Å2 / Biso min: 17.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.08 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: final / Resolution: 2.15→33.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4604 0 12 207 4823
Biso mean--37.27 32.66 -
Num. residues----585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0194751
X-RAY DIFFRACTIONr_bond_other_d0.0020.024487
X-RAY DIFFRACTIONr_angle_refined_deg1.061.966458
X-RAY DIFFRACTIONr_angle_other_deg0.848310357
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8625591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.24524.35223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97315802
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0571525
X-RAY DIFFRACTIONr_chiral_restr0.0590.2713
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215371
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021058
X-RAY DIFFRACTIONr_mcbond_it0.9883.452347
X-RAY DIFFRACTIONr_mcbond_other0.9893.4482345
X-RAY DIFFRACTIONr_mcangle_it1.8125.1662928
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 139 -
Rwork0.355 2747 -
all-2886 -
obs--99.76 %

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