[English] 日本語
Yorodumi
- PDB-1a2o: STRUCTURAL BASIS FOR METHYLESTERASE CHEB REGULATION BY A PHOSPHOR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1a2o
TitleSTRUCTURAL BASIS FOR METHYLESTERASE CHEB REGULATION BY A PHOSPHORYLATION-ACTIVATED DOMAIN
ComponentsCHEB METHYLESTERASE
KeywordsBACTERIAL CHEMOTAXIS / ADAPTATION / 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 / Response regulator / 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 / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDjordjevic, S. / Goudreau, P.N. / Xu, Q. / Stock, A.M. / West, A.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Structural basis for methylesterase CheB regulation by a phosphorylation-activated domain.
Authors: Djordjevic, S. / Goudreau, P.N. / Xu, Q. / Stock, A.M. / West, A.H.
History
DepositionJan 6, 1998Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CHEB METHYLESTERASE
B: CHEB METHYLESTERASE


Theoretical massNumber of molelcules
Total (without water)75,1982
Polymers75,1982
Non-polymers00
Water7,404411
1
A: CHEB METHYLESTERASE


Theoretical massNumber of molelcules
Total (without water)37,5991
Polymers37,5991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CHEB METHYLESTERASE


Theoretical massNumber of molelcules
Total (without water)37,5991
Polymers37,5991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)163.830, 100.460, 53.120
Angle α, β, γ (deg.)90.00, 98.63, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.933, -0.099, -0.346), (0.082, -0.995, 0.062), (-0.35, 0.029, 0.936)84.71128, 153.27753, 37.15702
2given(-0.956, -0.056, -0.29), (0.054, -0.998, 0.012), (-0.29, -0.004, 0.957)81.73852, 154.30302, 38.53921

-
Components

#1: Protein CHEB METHYLESTERASE


Mass: 37598.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Cellular location: CYTOPLASM / Plasmid: PME30 / Cell (production host): HB101 / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli)
References: UniProt: P04042, protein-glutamate methylesterase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 2.87 Å3/Da / Density % sol: 57.17 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
21.5 M1dropLi2SO4
30.1 Mimidazole1drop
41.45 M1reservoirLi2SO4
50.1 Mimidazole1reservoir
610 mM1reservoirMgCl2
75 mM1reservoirNaN3
1protein1drop0.001ml

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jan 1, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→15 Å / Num. obs: 32281 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 38.4 Å2 / Rsym value: 0.054 / Net I/σ(I): 7.5
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 4.1 / Rsym value: 0.163 / % possible all: 98.5
Reflection
*PLUS
Num. measured all: 97667 / Rmerge(I) obs: 0.054

-
Processing

Software
NameVersionClassification
X-PLORmodel building
REFMACrefinement
X-PLORrefinement
DENZOdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CHD

1chd


Resolution: 2.4→10 Å / Cross valid method: FREE R / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rwork0.222 ---
obs0.225 32281 96.9 %-
Rfree--5 %RANDOM
Displacement parametersBiso mean: 23.7 Å2
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5200 0 0 411 5611
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.02
X-RAY DIFFRACTIONp_angle_d0.0310.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0540.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.5582
X-RAY DIFFRACTIONp_mcangle_it2.663
X-RAY DIFFRACTIONp_scbond_it1.5332
X-RAY DIFFRACTIONp_scangle_it2.5553
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1070.15
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor6.93
X-RAY DIFFRACTIONp_staggered_tor22.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor36.320
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection all: 32281 / Rfactor all: 0.222 / Rfactor Rfree: 0.288
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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