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- PDB-1fmf: REFINED SOLUTION STRUCTURE OF THE (13C,15N-LABELED) B12-BINDING S... -

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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 L-glutamate catabolic process / methylaspartate mutase activity / L-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
Revision 1.5May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: METHYLASPARTATE MUTASE S CHAIN


Theoretical massNumber of molelcules
Total (without water)14,7641
Polymers14,7641
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)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

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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

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Experimental details

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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.

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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 / Pressure: 1 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

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

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