[English] 日本語
Yorodumi
- PDB-1qu7: FOUR HELICAL-BUNDLE STRUCTURE OF THE CYTOPLASMIC DOMAIN OF A SERI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qu7
TitleFOUR HELICAL-BUNDLE STRUCTURE OF THE CYTOPLASMIC DOMAIN OF A SERINE CHEMOTAXIS RECEPTOR
ComponentsMETHYL-ACCEPTING CHEMOTAXIS PROTEIN I
KeywordsSIGNALING PROTEIN / SERINE / CHEMOTAXIS / FOUR HELICAL-BUNDLE
Function / homology
Function and homology information


regulation of protein histidine kinase activity / detection of chemical stimulus / methyl accepting chemotaxis protein complex / regulation of bacterial-type flagellum-dependent cell motility / regulation of chemotaxis / signal complex assembly / receptor clustering / cell motility / cellular response to amino acid stimulus / chemotaxis ...regulation of protein histidine kinase activity / detection of chemical stimulus / methyl accepting chemotaxis protein complex / regulation of bacterial-type flagellum-dependent cell motility / regulation of chemotaxis / signal complex assembly / receptor clustering / cell motility / cellular response to amino acid stimulus / chemotaxis / transmembrane signaling receptor activity / signal transduction / identical protein binding / plasma membrane
Similarity search - Function
Methyl-accepting chemotaxis protein / Methyl-accepting chemotaxis protein, four helix bundle domain superfamily / Homologues of the ligand binding domain of Tar / Chemotaxis methyl-accepting receptor, methyl-accepting site / Bacterial chemotaxis sensory transducers signature. / Chemotaxis methyl-accepting receptor Tar-related, ligand-binding / Tar ligand binding domain homologue / Chemotaxis methyl-accepting receptor / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain ...Methyl-accepting chemotaxis protein / Methyl-accepting chemotaxis protein, four helix bundle domain superfamily / Homologues of the ligand binding domain of Tar / Chemotaxis methyl-accepting receptor, methyl-accepting site / Bacterial chemotaxis sensory transducers signature. / Chemotaxis methyl-accepting receptor Tar-related, ligand-binding / Tar ligand binding domain homologue / Chemotaxis methyl-accepting receptor / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Methyl-accepting chemotaxis protein I
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsKim, K.K. / Yokota, H. / Kim, S.-H.
CitationJournal: Nature / Year: 1999
Title: Four-helical-bundle structure of the cytoplasmic domain of a serine chemotaxis receptor.
Authors: Kim, K.K. / Yokota, H. / Kim, S.H.
History
DepositionJul 7, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: METHYL-ACCEPTING CHEMOTAXIS PROTEIN I
B: METHYL-ACCEPTING CHEMOTAXIS PROTEIN I


Theoretical massNumber of molelcules
Total (without water)47,4832
Polymers47,4832
Non-polymers00
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7910 Å2
ΔGint-83 kcal/mol
Surface area24470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.440, 132.440, 134.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

-
Components

#1: Protein METHYL-ACCEPTING CHEMOTAXIS PROTEIN I


Mass: 23741.311 Da / Num. of mol.: 2 / Fragment: CYTOPLASMIC DOMAIN (RESIDUE 286-526)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / References: UniProt: P02942
#2: Water ChemComp-HOH / water / 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: 4.78 Å3/Da / Density % sol: 74.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MPD, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: sparse matrix method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11 mMEDTA11
225 mMHEPES11pH7.4
35-10 mg/ml11
40.1 MN-[2-acetamide]-2-iminodiacetic acid12pH6.5
515-20 %MPD12
60.2 Msodium citrate12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.6→100 Å / Num. obs: 40467 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 3.84 % / Biso Wilson estimate: 54.6 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 4.9
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.745 / % possible all: 74
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 30 Å / Observed criterion σ(I): 0 / Redundancy: 3.84 % / Rmerge(I) obs: 0.125 / Biso Wilson estimate: 54.6 Å2
Reflection shell
*PLUS
Highest resolution: 2.6 Å / Rmerge(I) obs: 0.745

-
Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
MAR345data collection
SCALEPACKdata scaling
RefinementResolution: 2.6→100 Å / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
Details: THE DISTRIBUTION OF THE INTENSITIES OF DIFFRACTION PATTERN WAS VERY ANISOTROPIC : 2.6 A ALONG C-AXIS, 3.5 A ALONG A,B AXIS. SINCE DIFFRACTION INTENSITIES ARE ANISOTROPIC, REFLECTIONS IN ...Details: THE DISTRIBUTION OF THE INTENSITIES OF DIFFRACTION PATTERN WAS VERY ANISOTROPIC : 2.6 A ALONG C-AXIS, 3.5 A ALONG A,B AXIS. SINCE DIFFRACTION INTENSITIES ARE ANISOTROPIC, REFLECTIONS IN RESOLUTION RANGE OF 30.0 - 3.5 A ALONG A AND B AXES, AND 2.6 A ALONG C-AXIS WERE USED FOR REFINEMENT.
RfactorNum. reflectionSelection details
Rfree0.276 1066 5 % RANDOM SELECTION
Rwork0.243 --
obs0.243 21860 -
Refinement stepCycle: LAST / Resolution: 2.6→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3243 0 0 187 3430
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 30 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.243 / Rfactor Rfree: 0.276 / Rfactor Rwork: 0.243
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.51

+
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