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- PDB-2gtv: NMR structure of monomeric chorismate mutase from Methanococcus j... -

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Basic information

Entry
Database: PDB / ID: 2gtv
TitleNMR structure of monomeric chorismate mutase from Methanococcus jannaschii
Componentschorismate mutase
KeywordsISOMERASE / four-helix bundle
Function / homology
Function and homology information


salicylic acid biosynthetic process / chorismate metabolic process / chorismate mutase / chorismate mutase activity / identical protein binding
Similarity search - Function
Chorismate mutase, archaeal / Chorismate mutase / Chorismate mutase domain superfamily / Chorismate Mutase Domain, subunit A / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase type II superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-TSA / Chorismate mutase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodSOLUTION NMR / simulated annealing
AuthorsVogeli, B.R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2007
Title: Structure and dynamics of a molten globular enzyme.
Authors: Pervushin, K. / Vamvaca, K. / Vogeli, B. / Hilvert, D.
History
DepositionApr 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: chorismate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7412
Polymers12,5131
Non-polymers2281
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / -structures with the least restraint violations
RepresentativeModel #1random choice, due to similarity of all

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Components

#1: Protein chorismate mutase / / E.C.5.4.99.5 / CM / Hypothetical protein MJ0246


Mass: 12512.517 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Production host: Escherichia coli (E. coli) / Strain (production host): KA13 / References: UniProt: Q57696, chorismate mutase
#2: Chemical ChemComp-TSA / 8-HYDROXY-2-OXA-BICYCLO[3.3.1]NON-6-ENE-3,5-DICARBOXYLIC ACID


Mass: 228.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12O6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111standard suite for NMR protein structure determination
122standard suite for NMR protein structure determination

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6mM U-15N,13C, 20mM sodium phosphate, 50mM NaCl95% H20, 10% D20
20.05mM U-15N,13C, 20mM sodium phosphate, 50mM NaCl95% H20, 10% D20
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150mM NaCl 6.5 ambient 293 K
250mM NaCl 6.5 ambient 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE9002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1bruker biospin agcollection
X-PLORX-PLOR-NIH 2.9 4aschwieters, kuszewski, tjandra, clorestructure solution
PROSAguntertprocessing
CARA0.9.9kellerdata analysis
X-PLORX-PLOR-NIH 2.9 4aschwieters, kuszewski, tjandra, clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: random choice, due to similarity of all
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers submitted total number: 10

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