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- PDB-4u7n: Inactive structure of histidine kinase -

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Basic information

Entry
Database: PDB / ID: 4u7n
TitleInactive structure of histidine kinase
ComponentsHistidine protein kinase sensor protein
KeywordsTRANSFERASE / Histidine kinase
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
histidine kinase / :
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsCai, Y. / Hu, X. / Sang, J.
Funding support China, 1items
OrganizationGrant numberCountry
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
DepositionJul 31, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
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 / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histidine protein kinase sensor protein
B: Histidine protein kinase sensor protein


Theoretical massNumber of molelcules
Total (without water)63,3072
Polymers63,3072
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-25 kcal/mol
Surface area21960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.599, 91.599, 97.901
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Histidine protein kinase sensor protein


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 (bacteria) / Strain: JDM1 / Gene: hpk1, JDM1_0052 / Production host: Escherichia coli (E. coli) / References: UniProt: C6VIM1, UniProt: A0A0M3KKX3*PLUS

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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: 4.06 Å3/Da / Density % sol: 69.69 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: Ammonium sulfate, PEG 4000 / PH range: 5.6-6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3→25 Å / Num. obs: 36426 / % possible obs: 99.7 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 37.594
Reflection shellResolution: 3→3.05 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2 / % possible all: 99.6

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U7O

4u7o


Resolution: 3.2→23.387 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 34.07 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2848 3162 10.57 %
Rwork0.2509 --
obs0.2546 29907 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→23.387 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3394 0 0 0 3394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083450
X-RAY DIFFRACTIONf_angle_d1.174657
X-RAY DIFFRACTIONf_dihedral_angle_d15.981291
X-RAY DIFFRACTIONf_chiral_restr0.041530
X-RAY DIFFRACTIONf_plane_restr0.004595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.24770.38792040.34281096X-RAY DIFFRACTION100
3.2477-3.29830.42771760.35651126X-RAY DIFFRACTION99
3.2983-3.35220.2232640.31031268X-RAY DIFFRACTION100
3.3522-3.40990.37041160.31051160X-RAY DIFFRACTION100
3.4099-3.47170.34891880.30131104X-RAY DIFFRACTION99
3.4717-3.53820.36922040.30551162X-RAY DIFFRACTION100
3.5382-3.610200.31011271X-RAY DIFFRACTION100
3.6102-3.68840.36642080.27461110X-RAY DIFFRACTION99
3.6884-3.77390.31991840.30491087X-RAY DIFFRACTION100
3.7739-3.867800.25931344X-RAY DIFFRACTION100
3.8678-3.97190.31261920.26791138X-RAY DIFFRACTION99
3.9719-4.08820.2891950.27231088X-RAY DIFFRACTION100
4.0882-4.21940.41411480.2541210X-RAY DIFFRACTION100
4.2194-4.36930.2901440.27431240X-RAY DIFFRACTION99
4.3693-4.5430.34641780.27571099X-RAY DIFFRACTION99
4.543-4.74810.21571890.24661119X-RAY DIFFRACTION99
4.7481-4.996200.22891262X-RAY DIFFRACTION98
4.9962-5.30580.29871670.24761153X-RAY DIFFRACTION99
5.3058-5.70990.34441910.25651110X-RAY DIFFRACTION99
5.7099-6.27450.31211920.26371103X-RAY DIFFRACTION100
6.2745-7.159500.23111341X-RAY DIFFRACTION100
7.1595-8.93580.24031760.20241131X-RAY DIFFRACTION99
8.9358-23.3880.20431460.21441023X-RAY DIFFRACTION89
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)
11.1619-0.913-0.1941.39310.1753.46270.41480.1575-0.6018-0.19110.1321-0.0740.2729-0.88740.0591.188-0.06560.00510.67040.19851.0774-4.77927.6755-16.0236
23.42821.5764-0.09163.9941-2.26851.51590.613-0.60620.3613-0.4306-0.9591-0.39541.19081.9937-0.26831.20450.80740.01541.65590.34570.8285-17.465148.8679-26.5245
31.65560.46130.21142.5864-1.41722.393-0.03230.08880.36850.39220.61730.751-0.1771-0.7514-0.65341.06220.06090.08190.51770.19541.0235-3.867225.6142-7.3201
43.0417-0.8052-0.64953.5937-1.6581.34540.61860.9381-0.6454-0.0557-0.7874-0.2449-1.07731.3422-0.04951.2336-0.6390.02161.64720.26470.8488-17.55444.22142.8839
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 386 THROUGH 446 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 447 THROUGH 610 )
3X-RAY DIFFRACTION3CHAIN B AND (RESID 386 THROUGH 444 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 445 THROUGH 610 )

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