[English] 日本語
Yorodumi
- PDB-1chd: CHEB METHYLESTERASE DOMAIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1chd
TitleCHEB METHYLESTERASE DOMAIN
ComponentsCHEB METHYLESTERASE
KeywordsCARBOXYL METHYLESTERASE / CHEMOTAXIS PROTEIN / SERINE HYDROLASE
Function / homology
Function and homology information


protein-glutamate methylesterase / protein-glutamate methylesterase activity / protein-glutamine glutaminase activity / protein-glutamine glutaminase / phosphorelay response regulator activity / chemotaxis / cytoplasm
Similarity search - Function
Methylesterase CheB, C-terminal domain / Signal transduction response regulator, chemotaxis, protein-glutamate methylesterase / Protein-glutamate methylesterase/protein-glutamine glutaminase, CheB type / Methylesterase CheB, C-terminal / CheB methylesterase / CheB-type methylesterase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...Methylesterase CheB, C-terminal domain / Signal transduction response regulator, chemotaxis, protein-glutamate methylesterase / Protein-glutamate methylesterase/protein-glutamine glutaminase, CheB type / Methylesterase CheB, C-terminal / CheB methylesterase / CheB-type methylesterase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein-glutamate methylesterase/protein-glutamine glutaminase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.75 Å
AuthorsWest, A.H. / Martinez-Hackert, E. / Stock, A.M.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Crystal structure of the catalytic domain of the chemotaxis receptor methylesterase, CheB.
Authors: West, A.H. / Martinez-Hackert, E. / Stock, A.M.
#1: Journal: To be Published
Title: Purification, Crystallization, and Preliminary X-Ray Diffraction Analyses of the Bacterial Chemotaxis Receptor Modifying Enzymes
Authors: West, A.H. / Djordjevic, S. / Martinez-Hackert, E. / Stock, A.M.
#2: Journal: Biochim.Biophys.Acta / Year: 1992
Title: Evidence that the Methylesterase of Bacterial Chemotaxis May be a Serine Hydrolase
Authors: Krueger, J.K. / Stock, J. / Schutt, C.E.
#3: Journal: Annu.Rev.Biophys.Biophys.Chem. / Year: 1991
Title: Bacterial Chemotaxis and the Molecular Logic of Intracellular Signal Transduction Networks
Authors: Stock, J.B. / Lukat, G.S. / Stock, A.M.
#4: Journal: J.Biol.Chem. / Year: 1985
Title: Multiple Forms of the Cheb Methylesterase in Bacterial Chemosensing
Authors: Simms, S.A. / Keane, M.G. / Stock, J.
History
DepositionMar 9, 1995Processing site: BNL
Revision 1.0Jan 29, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 650HELIX HELIX DETERMINATION METHOD: H BONDS, DIHEDRAL ANGLES, KABSCH AND SANDER ALGORITHM, AND VISUAL ...HELIX HELIX DETERMINATION METHOD: H BONDS, DIHEDRAL ANGLES, KABSCH AND SANDER ALGORITHM, AND VISUAL INSPECTION HELIX_ID: L1,PART OF CONNECTING LOOP BETWEEN BETA STRAND 2 AND HELIX B. HELIX_ID: L2,PART OF CONNECTING LOOP BETWEEN BETA STRAND 6 AND HELIX C. HELIX_ID: L3,PART OF CONNECTING LOOP BETWEEN BETA STRAND 9 AND HELIX F. HELIX_ID: L4,PART OF CONNECTING LOOP BETWEEN BETA STRAND 8 AND HELIX E.
Remark 700SHEET SHEET SHEET_ID: SH1, H BONDS, DIHEDRAL ANGLES, KABSCH AND SANDER ALGORITHM, AND VISUAL ...SHEET SHEET SHEET_ID: SH1, H BONDS, DIHEDRAL ANGLES, KABSCH AND SANDER ALGORITHM, AND VISUAL INSPECTION. CENTRAL PARALLEL BETA SHEET. SHEET_ID: SH2, ANTIPARALLEL BETA MOTIF THAT FLANKS ONE SIDE OF THE CENTRAL SEVEN-STRANDED BETA SHEET.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CHEB METHYLESTERASE


Theoretical massNumber of molelcules
Total (without water)21,4581
Polymers21,4581
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.380, 63.380, 87.010
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Atom site foot note1: CIS PROLINE - PRO 258

-
Components

#1: Protein CHEB METHYLESTERASE


Mass: 21457.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: CHEB / Plasmid: PCP1 (PUC12 VECTOR) / Gene (production host): CHEB / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA
References: UniProt: P04042, protein-glutamate methylesterase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTURN TURN TYPES CLASSIFIED ACCORDING TO RICHARDSON, J.S (1981) ADVAN. PROT. CHEM., 34, 167-340.
Source detailsMOLECULE_NAME: CHEB METHYLESTERASE DOMAIN. DETAILS OF CONSTRUCTION OF EXPRESSION PLASMID AND ...MOLECULE_NAME: CHEB METHYLESTERASE DOMAIN. DETAILS OF CONSTRUCTION OF EXPRESSION PLASMID AND PROTEIN PURIFICATION ARE DESCRIBED IN WEST, A.H. ET AL. (1995) PROTEINS: STR. FUNC. GENET., IN PRESS.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.65 %
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.0-1.2 Mammonium sulfate1reservoir
20.1 MTris-HCl1reservoir
312 %(v/v)glycerol1reservoir
41.4 mM2-mercaptoethanol1reservoir
55 mM1reservoirNaN3

-
Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Aug 16, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 19729 / % possible obs: 93.6 % / Observed criterion σ(I): 3 / Redundancy: 2.4 % / Rmerge(I) obs: 0.045
Reflection
*PLUS
Highest resolution: 1.75 Å / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
% possible obs: 89.3 % / Rmerge(I) obs: 0.154 / Mean I/σ(I) obs: 5

-
Processing

Software
NameClassification
ARP/wARPmodel building
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.75→8 Å / σ(F): 0
Details: UNUSUAL DIHEDRAL ANGLES (PHI= -140.17 AND PSI= -120.83) ARE OBSERVED FOR SER 164 WHICH MAY ACCOUNT FOR THE CLOSE CONTACT AS AN ACTIVE SITE RESIDUE AND IS PROPOSED TO BE INVOLVED IN THE ...Details: UNUSUAL DIHEDRAL ANGLES (PHI= -140.17 AND PSI= -120.83) ARE OBSERVED FOR SER 164 WHICH MAY ACCOUNT FOR THE CLOSE CONTACT AS AN ACTIVE SITE RESIDUE AND IS PROPOSED TO BE INVOLVED IN THE CATALYSIS OF METHYL ESTER HYDROLYSIS. PHI/PSI ANGLES THAT LIE OUTSIDE THE EXPECTED RANGE HAVE BEEN OBSERVED FOR MANY OTHER ACTIVE SITE SERINE NUCLEOPHILES IN HYDROLYTIC ENZYMES OF THIS CLASS.
RfactorNum. reflection
Rfree0.23 -
obs0.182 16951
Displacement parametersBiso mean: 13.19 Å2
Refinement stepCycle: LAST / Resolution: 1.75→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1469 0 0 123 1592
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it0.4011
X-RAY DIFFRACTIONo_mcangle_it0.6821.5
X-RAY DIFFRACTIONo_scbond_it0.7041
X-RAY DIFFRACTIONo_scangle_it1.1521.5
Software
*PLUS
Name: ARP/PROLSQ/X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.02
X-RAY DIFFRACTIONp_angle_d0.030.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_planar_d0.030.02
X-RAY DIFFRACTIONp_plane_restr0.0090.02
X-RAY DIFFRACTIONp_chiral_restr0.1120.15
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

+
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