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- PDB-5is1: Crystal structure of the extracellular domain of sensor histidine... -

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Basic information

Entry
Database: PDB / ID: 5is1
TitleCrystal structure of the extracellular domain of sensor histidine kinase YycG from Staphylococcus aureus at 2.0 Angstrom resolution
ComponentsHistidine kinase
KeywordsTRANSFERASE / PAS/PDC domain / sensor histidine kinase / nest motif / membrane protein
Function / homology
Function and homology information


osmosensory signaling via phosphorelay pathway / phosphorelay response regulator activity / phosphorelay sensor kinase activity / histidine kinase / protein kinase activator activity / 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 / Histidine kinase/HSP90-like ATPase / PAS domain / PAS-associated, C-terminal ...: / Periplasmic sensor-like domain superfamily / : / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / Histidine kinase/HSP90-like ATPase / PAS domain / PAS-associated, C-terminal / PAC domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / PAS domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Beta-Lactamase / PAS domain / PAS repeat profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / PAS domain superfamily / Histidine kinase-like ATPases / 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 / MOLECULAR REPLACEMENT / Resolution: 1.998 Å
AuthorsKim, T. / Choi, J. / Lee, S. / Kim, K.K.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Structural Studies on the Extracellular Domain of Sensor Histidine Kinase YycG from Staphylococcus aureus and Its Functional Implications
Authors: Kim, T. / Choi, J. / Lee, S. / Yeo, K.J. / Cheong, H.K. / Kim, K.K.
History
DepositionMar 15, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histidine kinase


Theoretical massNumber of molelcules
Total (without water)17,4001
Polymers17,4001
Non-polymers00
Water1,35175
1
A: Histidine kinase

A: Histidine kinase


Theoretical massNumber of molelcules
Total (without water)34,7992
Polymers34,7992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_665x-y+1,-y+1,-z+1/31
Unit cell
Length a, b, c (Å)50.610, 50.610, 93.145
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-269-

HOH

21A-270-

HOH

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Components

#1: Protein Histidine kinase / sensor histidine kinase YycG / PAS domain-containing sensor histidine kinase / Two-component sensor ...sensor histidine kinase YycG / PAS domain-containing sensor histidine kinase / Two-component sensor histidine kinase / Two-component sensor histidine kinase (YycG)


Mass: 17399.508 Da / Num. of mol.: 1 / Fragment: Extracellular domai, UNP residues 33-182
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: RN4220
Gene: walK, walK_1, AL493_01420, AL498_11610, AL508_14645, AM595_00105, ASU36_11995, AUC48_00105, AUC49_00105, AUC50_00105, BN1321_430109, CH51_00105, EQ80_000105, ER12_000105, ERS092844_02460, ...Gene: walK, walK_1, AL493_01420, AL498_11610, AL508_14645, AM595_00105, ASU36_11995, AUC48_00105, AUC49_00105, AUC50_00105, BN1321_430109, CH51_00105, EQ80_000105, ER12_000105, ERS092844_02460, ERS093009_00906, ERS179246_01836, ERS195423_01765, ERS365775_01678, ERS410449_00558, ERS411009_01438, ERS411017_01103, ERS445051_00023, ERS445052_00659, FE68_05490, NI36_00110, RL02_04070, RT87_00105, SA7112_13655, SASCBU26_00023
Production host: Escherichia coli (E. coli)
References: UniProt: V5YQR2, UniProt: Q2G2U4*PLUS, histidine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 1.98 Å3/Da / Density % sol: 37.85 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 6
Details: 40-55% (w/v) PEG 400, 100mM 2-(N-morpholino)ethanesulfonic acid (MES) pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.998→20 Å / Num. obs: 9779 / % possible obs: 99.4 % / Redundancy: 10.3 % / Biso Wilson estimate: 41.92 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 71.355
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2-2.0710.50.3311100
2.07-2.1510.70.2391100
2.15-2.2510.70.1641100
2.25-2.3710.70.1271100
2.37-2.5210.70.0981100
2.52-2.7110.60.0721100
2.71-2.9910.50.0581100
2.99-3.4210.30.051100
3.42-4.39.90.045199.9
4.3-208.70.045194.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.998→19.829 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.87
RfactorNum. reflection% reflection
Rfree0.2286 986 10.11 %
Rwork0.2035 --
obs0.206 9749 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.55 Å2 / Biso mean: 54.0375 Å2 / Biso min: 18.17 Å2
Refinement stepCycle: final / Resolution: 1.998→19.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1150 0 0 75 1225
Biso mean---69.71 -
Num. residues----142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141184
X-RAY DIFFRACTIONf_angle_d1.3851594
X-RAY DIFFRACTIONf_chiral_restr0.079178
X-RAY DIFFRACTIONf_plane_restr0.005208
X-RAY DIFFRACTIONf_dihedral_angle_d15.77461
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 (%)
1.9982-2.10340.18321370.130312311368100
2.1034-2.2350.19071360.147112271363100
2.235-2.40730.21031430.158812481391100
2.4073-2.64910.23331370.173212441381100
2.6491-3.03120.20861410.185612511392100
3.0312-3.81460.23471430.208412721415100
3.8146-19.83010.241490.23061290143996

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