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- PDB-1id8: NMR STRUCTURE OF GLUTAMATE MUTASE (B12-BINDING SUBUNIT) COMPLEXED... -

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Basic information

Entry
Database: PDB / ID: 1id8
TitleNMR STRUCTURE OF GLUTAMATE MUTASE (B12-BINDING SUBUNIT) COMPLEXED WITH THE VITAMIN B12 NUCLEOTIDE
ComponentsMETHYLASPARTATE MUTASE S CHAIN
KeywordsISOMERASE / Coenzyme B12 / Ligand Binding / Nucleotide / Protein NMR spectroscopy / Protein folding
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
Chem-DBI / 2-HYDROXY-PROPYL-AMMONIUM / Glutamate mutase sigma subunit
Similarity search - Component
Biological speciesClostridium tetanomorphum (bacteria)
MethodSOLUTION NMR / restrained simulated annealing, molecular dynamics, energy minimazation
AuthorsTollinger, M. / Eichmuller, C. / Konrat, R. / Huhta, M.S. / Marsh, E.N.G. / Krautler, B.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: The B(12)-binding subunit of glutamate mutase from Clostridium tetanomorphum traps the nucleotide moiety of coenzyme B(12).
Authors: Tollinger, M. / Eichmuller, C. / Konrat, R. / Huhta, M.S. / Marsh, E.N. / Krautler, B.
#1: 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.
#2: 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. / Krautler, B.
History
DepositionApr 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: METHYLASPARTATE MUTASE S CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1983
Polymers14,7641
Non-polymers4342
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 30structures with the least restraint violations
RepresentativeModel #9fewest violations

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Components

#1: Protein METHYLASPARTATE MUTASE S CHAIN / GLUTAMATE MUTASE


Mass: 14763.856 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium tetanomorphum (bacteria) / Plasmid: PT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q05488, methylaspartate mutase
#2: Chemical ChemComp-FOP / 2-HYDROXY-PROPYL-AMMONIUM / F-LOOP OF VITAMIN B12


Mass: 76.118 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H10NO
#3: Chemical ChemComp-DBI / PHOSPHORIC ACID MONO-[5-(5,6-DIMETHYL-BENZOIMIDAZOL-1-YL)-4-HYDROXY-2-HYDROXYMETHYL-TETRAHYDRO-FURAN-3-YL] ESTER / DIMETHYLBENZIMIDAZOLE-NUCLEOTIDE


Mass: 358.284 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H19N2O7P

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1.5mM MutS U-15N; 18.0mM B12-Nucleotide; 10mM potassium phosphate buffer; 90% H2O, 10%D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 10mM potassium phosphate / pH: 6 / Pressure: ambient / 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
ANSIG3.3Kraulisdata analysis
NMRPipeDelaglioprocessing
X-PLOR3.1Brungerrefinement
RefinementMethod: restrained simulated annealing, molecular dynamics, energy minimazation
Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 30 / Conformers submitted total number: 15

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