[English] 日本語
Yorodumi
- PDB-1b3q: CRYSTAL STRUCTURE OF CHEA-289, A SIGNAL TRANSDUCING HISTIDINE KINASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1b3q
TitleCRYSTAL STRUCTURE OF CHEA-289, A SIGNAL TRANSDUCING HISTIDINE KINASE
ComponentsPROTEIN (CHEMOTAXIS PROTEIN CHEA)
KeywordsTRANSFERASE / HISTINE KINASE / SIGNAL TRANSDUCTION / CHEMOTAXIS / MULTI-DOMAINS PROTEIN
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / chemotaxis / protein domain specific binding / ATP binding / cytoplasm
Similarity search - Function
Histidine kinase CheA-like, homodimeric domain / CheA-289, Domain 4 / Chemotaxis protein CheA, P2 response regulator-binding domain superfamily / Chemotaxis protein CheA, P2 response regulator-binding / P2 response regulator binding domain / Histidine kinase CheA-like, homodimeric domain / CheY-binding domain of CheA / Histidine kinase CheA-like, homodimeric domain superfamily / Signal transducing histidine kinase, homodimeric domain / Signal transducing histidine kinase, homodimeric domain ...Histidine kinase CheA-like, homodimeric domain / CheA-289, Domain 4 / Chemotaxis protein CheA, P2 response regulator-binding domain superfamily / Chemotaxis protein CheA, P2 response regulator-binding / P2 response regulator binding domain / Histidine kinase CheA-like, homodimeric domain / CheY-binding domain of CheA / Histidine kinase CheA-like, homodimeric domain superfamily / Signal transducing histidine kinase, homodimeric domain / Signal transducing histidine kinase, homodimeric domain / CheW-like domain profile. / CheW-like domain / CheW-like domain superfamily / CheW-like domain / Two component signalling adaptor domain / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / SH3 Domains / 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 / SH3 type barrels. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Helix Hairpins / Roll / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Chemotaxis protein CheA
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.6 Å
AuthorsBilwes, A.M. / Alex, L.A. / Crane, B.R. / Simon, M.I.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: Structure of CheA, a signal-transducing histidine kinase.
Authors: Bilwes, A.M. / Alex, L.A. / Crane, B.R. / Simon, M.I.
History
DepositionDec 14, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 15, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (CHEMOTAXIS PROTEIN CHEA)
B: PROTEIN (CHEMOTAXIS PROTEIN CHEA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,3304
Polymers84,9292
Non-polymers4012
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-76 kcal/mol
Surface area38070 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)61.800, 126.500, 75.100
Angle α, β, γ (deg.)90.00, 95.60, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein PROTEIN (CHEMOTAXIS PROTEIN CHEA)


Mass: 42464.340 Da / Num. of mol.: 2
Fragment: DIMERIZATION DOMAIN, KINASE DOMAIN AND REGULATORY DOMAIN
Mutation: Q545C, I521M, S522G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Cellular location: CYTOPLASM / Plasmid: PET28(A)+ / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q56310, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 65 %
Crystal growpH: 5.5
Details: 80MM SUCCINATE, PH 5.5, 20% MPD, 5% ISOPROPANOL, 4% PEG 8000
Components of the solutions
IDNameCrystal-IDSol-ID
180MM SUCCINATE PH 5.512
220% MPD12
35% ISOPROPANOL12
44% PEG 800012
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
180 mMsuccinate1reservoir
220 %MPD1reservoir
35 %isopropanol1reservoir
43-7 %PEG80001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.946, 0.999, 1.001
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 1, 1998
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9461
20.9991
31.0011
ReflectionResolution: 2.6→20 Å / Num. obs: 93352 / % possible obs: 92.6 % / Redundancy: 3 % / Biso Wilson estimate: 62.8 Å2 / Rsym value: 0.0068 / Net I/σ(I): 21
Reflection shellResolution: 2.6→2.7 Å / Mean I/σ(I) obs: 3.2 / Rsym value: 0.0344 / % possible all: 79.5
Reflection
*PLUS
Num. obs: 33278 / Num. measured all: 93352 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 79.5 % / Rmerge(I) obs: 0.344

-
Processing

Software
NameVersionClassification
PHASESphasing
MADPHSREFmodel building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
MADPHSREFphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1916 -RANDOM
Rwork0.213 ---
obs-33278 92.6 %-
Displacement parametersBiso mean: 60.3 Å2
Baniso -1Baniso -2Baniso -3
1-18.9 Å20 Å213.1 Å2
2--7.9 Å20 Å2
3---0.4 Å2
Refine analyzeLuzzati d res low obs: 20 Å
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5787 0 2 187 5976
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.6→2.7 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.0318 128 -
Rwork0.031 1743 -
obs--79.5 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
LS refinement shell
*PLUS
Rfactor Rfree: 0.318 / Rfactor Rwork: 0.31

+
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://pdbjlvh1.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