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- PDB-4zki: The crystal structure of Histidine Kinase YycG with ADP -

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Basic information

Entry
Database: PDB / ID: 4zki
TitleThe crystal structure of Histidine Kinase YycG with ADP
ComponentsHistidine kinase
KeywordsTRANSFERASE / Histidine Kinase / ADP
Function / homology
Function and homology information


cellular response to phosphate starvation / histidine kinase / phosphoprotein phosphatase activity / phosphorelay sensor kinase activity / nucleotide binding / plasma membrane
Similarity search - Function
Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / 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 ...Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / 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 / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / histidine kinase / :
Similarity search - Component
Biological speciesLactobacillus plantarum JDM1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.401 Å
AuthorsCai, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) China
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Conformational dynamics of the essential sensor histidine kinase WalK
Authors: Cai, Y. / Su, M. / Ahmad, A. / Hu, X. / Sang, J. / Kong, L. / Chen, X. / Wang, C. / Shuai, J. / Han, A.
History
DepositionApr 30, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 25, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histidine kinase
B: Histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7343
Polymers63,3072
Non-polymers4271
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-36 kcal/mol
Surface area22050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.499, 96.034, 119.351
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Histidine kinase / YycG


Mass: 31653.488 Da / Num. of mol.: 2 / Fragment: UNP residues 370-624
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum JDM1 (bacteria)
Strain: JDM1 / Gene: hpk1, JDM1_0052 / Production host: Escherichia coli (E. coli)
References: UniProt: C6VIM1, UniProt: A0A0M3KKX3*PLUS, 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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.8 / Details: 1.0 M Ammonium Sulfate, 1% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Type: OTHER / Wavelength: 0.97853 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 8921 / % possible obs: 99.8 % / Redundancy: 5.6 % / Net I/σ(I): 10

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4u7o

4u7o


Resolution: 3.401→48.819 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.222 449 5.06 %Random selection
Rwork0.2014 ---
obs0.2025 8881 99.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.401→48.819 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3555 0 27 0 3582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113642
X-RAY DIFFRACTIONf_angle_d1.4374915
X-RAY DIFFRACTIONf_dihedral_angle_d16.2411362
X-RAY DIFFRACTIONf_chiral_restr0.053553
X-RAY DIFFRACTIONf_plane_restr0.007625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.401-3.89290.27071500.22782733X-RAY DIFFRACTION99
3.8929-4.9040.21291490.18712777X-RAY DIFFRACTION100
4.904-48.82380.20741500.19982922X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.27040.3019-0.23350.6952-0.52640.32370.09580.0323-0.0495-0.25650.1239-0.0572-0.03960.07860.00980.4760.0495-0.00280.5624-0.0170.589111.1961-5.0018-21.0471
20.73570.25790.07410.5140.40650.3143-0.1207-0.0991-0.0330.18130.10640.0365-0.0579-0.0398-0.01480.34670.03780.04510.39390.04430.41432.1681-27.4879-28.8591
30.17690.06990.10590.3026-0.16050.1208-0.3244-0.49170.25310.37780.4611-0.4029-0.0218-0.17090.00030.52220.098-0.01480.44010.01040.46939.25580.3432-10.2924
40.7593-0.0582-0.21330.1243-0.02170.7638-0.48810.39780.18320.06710.2615-0.0381-0.6690.0333-0.21530.7263-0.0435-0.07670.49690.0670.534515.56370.49392.4149
50.599-0.6508-0.86042.7260.36521.45110.1308-0.0189-0.01510.07130.1732-0.82280.16160.14840.13550.4025-0.1024-0.10070.3960.02260.301917.9701-5.208111.4295
60.3161-0.25170.15880.45380.20810.29910.24080.1025-0.2427-0.2765-0.2068-0.19310.74370.1795-0.02710.8675-0.0763-0.08290.4679-0.00330.590823.0733-13.67574.5947
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 372 through 447 )
2X-RAY DIFFRACTION2chain 'A' and (resid 448 through 610 )
3X-RAY DIFFRACTION3chain 'B' and (resid 384 through 440 )
4X-RAY DIFFRACTION4chain 'B' and (resid 441 through 517 )
5X-RAY DIFFRACTION5chain 'B' and (resid 518 through 542 )
6X-RAY DIFFRACTION6chain 'B' and (resid 543 through 610 )

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