[English] 日本語
Yorodumi
- PDB-1fmf: REFINED SOLUTION STRUCTURE OF THE (13C,15N-LABELED) B12-BINDING S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fmf
TitleREFINED SOLUTION STRUCTURE OF THE (13C,15N-LABELED) B12-BINDING SUBUNIT OF GLUTAMATE MUTASE FROM CLOSTRIDIUM TETANOMORPHUM
ComponentsMETHYLASPARTATE MUTASE S CHAIN
KeywordsISOMERASE / nucleotide binding fold / Rossmann fold
Function / homology
Function and homology information


methylaspartate mutase / anaerobic glutamate catabolic process / methylaspartate mutase activity / glutamate catabolic process via L-citramalate / cobalamin binding / metal ion binding
Similarity search - Function
Glutamate mutase sigma subunit / Cobalamin-binding domain / B12 binding domain / Cobalamin-binding domain superfamily / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutamate mutase sigma subunit
Similarity search - Component
Biological speciesClostridium tetanomorphum (bacteria)
MethodSOLUTION NMR / distance geometry, simulated annealing, simulated annealing refinement, energy minimization
AuthorsHoffmann, B. / Konrat, R. / Tollinger, M. / Huhta, M. / Marsh, E.N.G. / Kraeutler, B.
Citation
Journal: Chembiochem / Year: 2001
Title: A protein pre-organized to trap the nucleotide moiety of coenzyme B(12): refined solution structure of the B(12)-binding subunit of glutamate mutase from Clostridium tetanomorphum.
Authors: Hoffmann, B. / Tollinger, M. / Konrat, R. / Huhta, M. / Marsh, E.N. / Krautler, B.
#1: Journal: Structure / Year: 1998
Title: How a protein prepares for B12-binding: structure and dynamics of the B12-binding subunit of glutamate mutase from Clostridium tetanomorphum
Authors: Tollinger, M. / Konrat, R. / Hilbert, B.H. / Marsh, E.N.G. / Kraeutler, B.
#2: Journal: J.Biol.Chem. / Year: 1994
Title: Adenosylcobalamin-dependent glutamate mutase from Clostridium tetanomorphum. Overexpression in Escherichia coli, purification and Characterization of the recombinant enzyme
Authors: Holloway, D.E. / Marsh, E.N.G.
History
DepositionAug 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: METHYLASPARTATE MUTASE S CHAIN


Theoretical massNumber of molelcules
Total (without water)14,7641
Polymers14,7641
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 200structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #16fewest violations

-
Components

#1: Protein METHYLASPARTATE MUTASE S CHAIN / GLUTAMATE MUTASE / MUTS


Mass: 14763.856 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium tetanomorphum (bacteria) / Plasmid: PMUTSX / Production host: Escherichia coli (E. coli) / References: UniProt: Q05488, methylaspartate mutase

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 13C-separated NOESY
1313D 15N-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

-
Sample preparation

DetailsContents: 1.5mM MutS U-98% 15N,13C; 11mM phosphate buffer; / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 11mM KXH3-XPO4 / pH: 6.0 / Pressure: 1 atm / Temperature: 299 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglioprocessing
ANSIG3.3Kraulisdata analysis
X-PLOR3.8.5.1Bruengerstructure solution
TALOS98.040.21.02Cornilescudata analysis
X-PLOR3.8.5.1Bruengerrefinement
RefinementMethod: distance geometry, simulated annealing, simulated annealing refinement, energy minimization
Software ordinal: 1
Details: The MutS structure models 1-15 are based on a total of 1792 restraints, 1553 are NOE-derived distance constraints, 184 dihedral angle restraints, 55 distance restraints from hydrogen bonds. ...Details: The MutS structure models 1-15 are based on a total of 1792 restraints, 1553 are NOE-derived distance constraints, 184 dihedral angle restraints, 55 distance restraints from hydrogen bonds. Backbone dihedral angles Phi and Psi were obtained by employing TALOS software [G. Cornilescu et al., J. Biomol. NMR 1999, 13, 289-302]. Phi and Psi torsion angle restraints for the MutS residues 23-30, which form a "nascent" helix [M. Tollinger et al., Structure 1998, 6, 1021-1033], were not used in structure calculations for MutS models 16-30.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 30

+
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