[English] 日本語
Yorodumi
- PDB-4zki: The crystal structure of Histidine Kinase YycG with ADP -

+
Open data


ID or keywords:

Loading...

-
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


histidine kinase / phosphorelay signal transduction system / kinase activity / nucleotide binding
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 ...: / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more