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- PDB-5c93: Histidine kinase with ATP -

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Basic information

Entry
Database: PDB / ID: 5c93
TitleHistidine kinase with ATP
ComponentsHistidine kinase
KeywordsTRANSFERASE / Histidine Kinase / ATP
Function / homology
Function and homology information


histidine kinase / kinase activity
Similarity search - Function
Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / Periplasmic sensor-like domain superfamily / 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, dimerisation/phosphotransfer (DHp) domain / Periplasmic sensor-like domain superfamily / 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-like ATPase, C-terminal domain / Heat Shock Protein 90 / PAS fold / PAS fold / 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 / Histidine kinase/HSP90-like ATPase superfamily / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Histidine kinase
Similarity search - Component
Biological speciesLactobacillus plantarum 16 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.518 Å
AuthorsCai, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Fundation of China 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
DepositionJun 26, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 27, 2016Provider: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,9418
Polymers58,5462
Non-polymers1,3956
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-91 kcal/mol
Surface area22940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.645, 97.757, 117.342
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: 29272.916 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 370-624
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum 16 (bacteria) / Gene: Lp16_0032 / Production host: Escherichia coli (E. coli) / References: UniProt: R9WYL1, histidine kinase
#2: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 1.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 21206 / % possible obs: 97.9 % / Redundancy: 4.7 % / Net I/σ(I): 25.3
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.04 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4u7o

4u7o


Resolution: 2.518→37.011 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2735 1039 4.93 %Random
Rwork0.2185 ---
obs0.2212 21072 95.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.518→37.011 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3659 0 82 6 3747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033811
X-RAY DIFFRACTIONf_angle_d0.8755056
X-RAY DIFFRACTIONf_dihedral_angle_d13.0361408
X-RAY DIFFRACTIONf_chiral_restr0.035566
X-RAY DIFFRACTIONf_plane_restr0.003648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5184-2.65110.42121560.33062562X-RAY DIFFRACTION88
2.6511-2.81710.34741030.30812805X-RAY DIFFRACTION94
2.8171-3.03460.32851560.26892941X-RAY DIFFRACTION100
3.0346-3.33980.31571560.25122922X-RAY DIFFRACTION100
3.3398-3.82260.30061560.22882801X-RAY DIFFRACTION94
3.8226-4.81440.22541560.18852879X-RAY DIFFRACTION96
4.8144-37.01480.24711560.18823123X-RAY DIFFRACTION99
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)
10.26110.0371-0.46860.4764-0.249-0.2553-0.0499-0.0814-0.0548-0.00920.1509-0.01170.1374-0.062300.5140.0422-0.03290.4924-0.04680.472111.5379-4.1784-20.6159
20.26130.17470.09870.513-0.59330.6719-0.0313-0.0175-0.1785-0.06670.1150.0866-0.21680.11160.00030.38010.02530.06530.34910.0340.40181.4884-26.8078-29.0272
30.0220.05370.0740.3508-0.02440.1781-0.1233-0.007-0.12240.37090.17520.0070.6073-0.0623-0.00010.51490.0673-0.05930.5303-0.00490.491910.9139-5.2076-10.2006
40.0292-0.0167-0.0240.21250.0591-0.0102-0.27820.084-0.00960.46830.2518-0.1457-0.0886-0.0478-0.00340.488-0.0052-0.00690.5666-0.03630.45999.72035.7144-9.4232
50.14180.0469-0.01750.222-0.07480.106-0.0352-0.16290.0696-0.0731-0.02680.0043-0.09490.0691-0.00640.50330.01480.04550.44620.03560.449318.59912.4578-0.8598
60.40450.130.32650.1216-0.50780.40180.2755-0.02160.03040.3004-0.1208-0.1932-0.033-0.10720.0410.585-0.084-0.14780.4020.01740.442216.5926-6.18937.5401
7-0.00680.0424-0.01510.03920.0158-0.00540.1658-0.03980.1372-0.22960.4035-0.1-0.26440.1937-01.20720.02380.05010.7481-0.08081.079118.1399-22.0519-1.7183
80.0472-0.15680.16980.4861-0.53020.61680.4493-0.14610.0646-0.2179-0.2324-0.1341.03320.70880.01990.7349-0.0028-0.06110.5235-0.00750.528825.5946-8.64716.8343
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 383 through 409 )
4X-RAY DIFFRACTION4chain 'B' and (resid 410 through 441 )
5X-RAY DIFFRACTION5chain 'B' and (resid 442 through 475 )
6X-RAY DIFFRACTION6chain 'B' and (resid 476 through 556 )
7X-RAY DIFFRACTION7chain 'B' and (resid 557 through 575 )
8X-RAY DIFFRACTION8chain 'B' and (resid 576 through 610 )

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