[English] 日本語
Yorodumi
- PDB-1vlz: UNCOUPLED PHOSPHORYLATION AND ACTIVATION IN BACTERIAL CHEMOTAXIS:... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vlz
TitleUNCOUPLED PHOSPHORYLATION AND ACTIVATION IN BACTERIAL CHEMOTAXIS: THE 2.1 ANGSTROM STRUCTURE OF A THREONINE TO ISOLEUCINE MUTANT AT POSITION 87 OF CHEY
ComponentsCHEY
KeywordsSIGNAL TRANSDUCTION PROTEIN / CHEY / 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 (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.05 Å
AuthorsGanguli, S. / Wang, H. / Matsumura, P. / Volz, K.
Citation
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.
#1: Journal: Biochemistry / Year: 1993
Title: Structural Conservation in the Chey Superfamily
Authors: Volz, K.
#2: Journal: J.Biol.Chem. / Year: 1991
Title: Crystal Structure of Escherichia Coli Chey Refined at 1.7-Angstrom Resolution
Authors: Volz, K. / Matsumura, P.
History
DepositionApr 21, 1995Processing site: BNL
Revision 1.0Jul 10, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CHEY
B: CHEY


Theoretical massNumber of molelcules
Total (without water)27,9862
Polymers27,9862
Non-polymers00
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.040, 72.470, 36.150
Angle α, β, γ (deg.)90.00, 109.06, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO A 110 / 2: CIS PROLINE - PRO B 110
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.04625, 0.26865, -0.96213), (0.09375, -0.96008, -0.26357), (-0.99452, -0.07801, -0.06959)
Vector: 43.19112, 25.73944, 64.56831)

-
Components

#1: Protein CHEY


Mass: 13993.189 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: CHEY / References: UniProt: P06143, UniProt: P0AE67*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.54 %
Crystal grow
*PLUS
Temperature: 37 ℃ / Method: mid-log phase / Details: Matsumura, P., (1984) J. Bacteriol., 160, 36.

-
Data collection

RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 15093 / % possible obs: 90.8 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.0457
Reflection
*PLUS
Highest resolution: 2.04 Å / Lowest resolution: 9999 Å / Num. measured all: 30935 / Rmerge(I) obs: 0.0457

-
Processing

Software
NameClassification
PROFFTrefinement
XENGENdata reduction
RefinementResolution: 2.05→10 Å / σ(F): 2
Details: SOLVENT. MOST WATER MOLECULES ARE WELL BEHAVED. A FEW WATERS WITH HIGH TEMPERATURE FACTORS AND CLOSE CONTACTS WITH OTHER WATERS MAY BE PARTIAL SITES. SOLVENT MOLECULES HOH A 214 AND HOH B ...Details: SOLVENT. MOST WATER MOLECULES ARE WELL BEHAVED. A FEW WATERS WITH HIGH TEMPERATURE FACTORS AND CLOSE CONTACTS WITH OTHER WATERS MAY BE PARTIAL SITES. SOLVENT MOLECULES HOH A 214 AND HOH B 203 ARE PROBABLY AMMONIUM IONS.
RfactorNum. reflection
obs0.156 13198
Displacement parametersBiso mean: 16.3 Å2
Refinement stepCycle: LAST / Resolution: 2.05→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1898 0 0 172 2070
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_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.8571
X-RAY DIFFRACTIONp_mcangle_it1.5131.5
X-RAY DIFFRACTIONp_scbond_it1.0441
X-RAY DIFFRACTIONp_scangle_it1.81.5
X-RAY DIFFRACTIONp_plane_restr0.0110.02
X-RAY DIFFRACTIONp_chiral_restr0.1430.15
X-RAY DIFFRACTIONp_singtor_nbd0.1880.5
X-RAY DIFFRACTIONp_multtor_nbd0.1940.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2270.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.13
X-RAY DIFFRACTIONp_staggered_tor15.815
X-RAY DIFFRACTIONp_orthonormal_tor27.620
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

+
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