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- PDB-1b1a: GLUTAMATE MUTASE (B12-BINDING SUBUNIT), NMR, MINIMIZED AVERAGE ST... -

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Basic information

Entry
Database: PDB / ID: 1b1a
TitleGLUTAMATE MUTASE (B12-BINDING SUBUNIT), NMR, MINIMIZED AVERAGE STRUCTURE
ComponentsGLUTAMATE MUTASE
KeywordsISOMERASE / GLUTAMATE MUTASE / B12-BINDING SUBUNIT
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 cochlearium (bacteria)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING, ENERGY MINIMIZATION
AuthorsHoffmann, B. / Konrat, R. / Bothe, H. / Buckel, W. / Kraeutler, B.
Citation
Journal: Eur.J.Biochem. / Year: 1999
Title: Structure and dynamics of the B12-binding subunit of glutamate mutase from Clostridium cochlearium.
Authors: Hoffmann, B. / Konrat, R. / Bothe, H. / Buckel, W. / Krautler, B.
#1: Journal: Fems Microbiol.Lett. / Year: 1994
Title: Cloning, Sequencing and Expression in Escherichia Coli of the Gene Encoding Component S of the Coenzyme B12-Dependent Glutamate Mutase from Clostridium Cochlearium
Authors: Zelder, O. / Beatrix, B. / Buckel, W.
History
DepositionNov 19, 1998Processing site: BNL
Revision 1.0Jul 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 10, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_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 / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUTAMATE MUTASE


Theoretical massNumber of molelcules
Total (without water)14,8301
Polymers14,8301
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 15MINIMIZED AVERAGE
Representative

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Components

#1: Protein GLUTAMATE MUTASE / GLMS


Mass: 14830.046 Da / Num. of mol.: 1 / Fragment: B12-BINDING SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium cochlearium (bacteria) / Description: DSM 1285 / Gene: GLMS / Plasmid: POZ3 / Gene (production host): GLMS / Production host: Escherichia coli (E. coli) / Strain (production host): MC4100 / References: UniProt: P80078, methylaspartate mutase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 15N HSQC
1212D X-FILT NOESY
1312D NOESY
1412D TOCSY
1513D 15N NOESY-HSQC
1613D 15N TOCSY-HSQC
1713D HNHA
NMR detailsText: MEAN STRUCTURE

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Sample preparation

DetailsContents: 10% H2O/90% D2O
Sample conditionsIonic strength: 10mM K2HPO4/KH2PO4 / pH: 7.4 / Pressure: ATMOSPHERIC atm / Temperature: 299 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
NMRPipestructure solution
ANSIGstructure solution
Felixstructure solution
X-PLOR3.1structure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING, ENERGY MINIMIZATION
Software ordinal: 1
NMR ensembleConformer selection criteria: MINIMIZED AVERAGE / Conformers calculated total number: 15 / Conformers submitted total number: 1

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