[English] 日本語
Yorodumi
- PDB-6chy: STRUCTURE OF CHEMOTAXIS PROTEIN CHEY -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6chy
TitleSTRUCTURE OF CHEMOTAXIS PROTEIN CHEY
ComponentsCHEY
KeywordsSIGNAL TRANSDUCTION PROTEIN / RESPONSE REGULATORS / TWO-COMPONENT SYSTEMS
Function / homology
Function and homology information


bacterial-type flagellum basal body, C ring / bacterial-type flagellum rotor complex / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / bacterial-type flagellum / regulation of chemotaxis / thermotaxis / internal peptidyl-lysine acetylation / phosphorelay response regulator activity ...bacterial-type flagellum basal body, C ring / bacterial-type flagellum rotor complex / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / bacterial-type flagellum / regulation of chemotaxis / thermotaxis / internal peptidyl-lysine acetylation / phosphorelay response regulator activity / protein acetylation / acetyltransferase activity / phosphorelay signal transduction system / chemotaxis / magnesium ion binding / signal transduction / cytosol / cytoplasm
Similarity search - Function
Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chemotaxis protein CheY / Chemotaxis protein CheY
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsZhu, X. / Rebello, J. / Matsumura, P. / Volz, K.
Citation
Journal: J.Biol.Chem. / Year: 1997
Title: Crystal structures of CheY mutants Y106W and T87I/Y106W. CheY activation correlates with movement of residue 106.
Authors: Zhu, X. / Rebello, J. / Matsumura, P. / Volz, K.
#1: Journal: J.Bacteriol. / Year: 1996
Title: Tyrosine 106 Plays an Important Role in Chemotaxis Signal Transduction in Escherichia Coli
Authors: Zhu, X. / Amsler, C.D. / Volz, K. / Matsumura, P.
#2: Journal: J.Biol.Chem. / Year: 1995
Title: Uncoupled Phosphorylation and Activation in Bacterial Chemotaxis. The 2.1-A Structure of a Threonine to Isoleucine Mutant at Position 87 of Chey
Authors: Ganguli, S. / Wang, H. / Matsumura, P. / Volz, K.
#3: Journal: Biochemistry / Year: 1993
Title: Structural Conservation in the Chey Superfamily
Authors: Volz, K.
#4: Journal: J.Biol.Chem. / Year: 1991
Title: Crystal Structure of Escherichia Coli Chey Refined at 1.7-A Resolution
Authors: Volz, K. / Matsumura, P.
History
DepositionAug 29, 1996Processing site: BNL
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / refine
Item: _refine.pdbx_starting_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CHEY
B: CHEY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1293
Polymers28,0322
Non-polymers961
Water3,189177
1
A: CHEY


Theoretical massNumber of molelcules
Total (without water)14,0161
Polymers14,0161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CHEY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1122
Polymers14,0161
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: CHEY
hetero molecules

B: CHEY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2254
Polymers28,0322
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area1490 Å2
ΔGint-45 kcal/mol
Surface area11590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.780, 76.700, 32.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-210-

HOH

21A-211-

HOH

31A-212-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.78822, -0.61539, 0.00058), (-0.6152, 0.78795, -0.02562), (0.01531, -0.02055, -0.99967)
Vector: 76.9536, 26.924, 36.8423)

-
Components

#1: Protein CHEY


Mass: 14016.225 Da / Num. of mol.: 2 / Mutation: T87I, Y106W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Plasmid: CHEY / Production host: Escherichia coli (E. coli) / References: UniProt: P06143, UniProt: P0AE67*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.14 Å3/Da / Density % sol: 42.47 %
Crystal growDetails: 18% PEG 3350 AND 0.2 M AMMONIUM SULFATE
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118 %PEG33501reservoir
20.2 Mammonium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.033
DetectorDetector: CCD
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionHighest resolution: 2.3 Å / Num. obs: 7861 / % possible obs: 72.5 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.051
Reflection shellResolution: 2.33→2.45 Å / % possible all: 43.2
Reflection
*PLUS
% possible obs: 73 % / Num. measured all: 28137

-
Processing

Software
NameClassification
MERLOTphasing
PROFFTrefinement
MADNESdata reduction
MADNESdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.185 --
obs-7698 72.5 %
Displacement parametersBiso mean: 11.04 Å2
Refinement stepCycle: LAST / Resolution: 2.33→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1951 0 5 177 2133
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0480.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0490.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.6051
X-RAY DIFFRACTIONp_mcangle_it1.0291.5
X-RAY DIFFRACTIONp_scbond_it0.5861
X-RAY DIFFRACTIONp_scangle_it0.9871.5
X-RAY DIFFRACTIONp_plane_restr0.0110.02
X-RAY DIFFRACTIONp_chiral_restr0.1630.15
X-RAY DIFFRACTIONp_singtor_nbd0.20.5
X-RAY DIFFRACTIONp_multtor_nbd0.2510.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2750.5
X-RAY DIFFRACTIONp_planar_tor23
X-RAY DIFFRACTIONp_staggered_tor20.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor27.720
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.33 Å / Lowest resolution: 2.45 Å / Total num. of bins used: 7 / Num. reflection obs: 1474 / Rfactor obs: 0.222

+
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