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- PDB-2mcf: NMR structure of TGAM_1934 -

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Basic information

Entry
Database: PDB / ID: 2mcf
TitleNMR structure of TGAM_1934
ComponentsTGAM_1934
KeywordsUNKNOWN FUNCTION / Tgam
Function / homologyRossmann fold - #11630 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesThermococcus gammatolerans (archaea)
MethodSOLUTION NMR / simulated annealing
AuthorsYang, Y. / Montet de Guillen, K. / Roumestand, C.
CitationJournal: Proteomics / Year: 2015
Title: Prioritizing targets for structural biology through the lens of proteomics: the archaeal protein TGAM_1934 from Thermococcus gammatolerans.
Authors: Yang, Y.S. / Fernandez, B. / Lagorce, A. / Aloin, V. / De Guillen, K.M. / Boyer, J.B. / Dedieu, A. / Confalonieri, F. / Armengaud, J. / Roumestand, C.
History
DepositionAug 19, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references / Structure summary
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TGAM_1934


Theoretical massNumber of molelcules
Total (without water)16,7581
Polymers16,7581
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)15 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein TGAM_1934


Mass: 16758.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus gammatolerans (archaea) / Strain: DSM 15229 / JCM 11827 / EJ3 / Gene: TGAM_1934 / Production host: Escherichia coli (E. coli) / References: UniProt: C5A217
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D CBCA(CO)NH
1413D 1H-15N NOESY
1513D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.5-0.8 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleUnits: mM / Component: protein-1 / Isotopic labeling: [U-100% 13C; U-100% 15N] / Conc. range: 0.5-0.8
Sample conditionsIonic strength: 0.2 / pH: 6.6 / Pressure: ambient / Temperature: 305 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR softwareName: CYANA / Version: 2.1 / Developer: Guntert, Mumenthaler and Wuthrich / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 15

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