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- PDB-2ka7: NMR solution structure of TM0212 at 40 C -

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Basic information

Entry
Database: PDB / ID: 2ka7
TitleNMR solution structure of TM0212 at 40 C
ComponentsGlycine cleavage system H protein
Keywordsstructural genomics / unknown function / PROTEIN / Lipoyl / PSI-2 / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG
Function / homology
Function and homology information


glycine decarboxylation via glycine cleavage system / glycine cleavage complex / cytosol
Similarity search - Function
Glycine cleavage system H-protein, subgroup / Glycine cleavage system H-protein / Glycine cleavage system H-protein/Simiate / Glycine cleavage H-protein / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif ...Glycine cleavage system H-protein, subgroup / Glycine cleavage system H-protein / Glycine cleavage system H-protein/Simiate / Glycine cleavage H-protein / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Glycine cleavage system H protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsPedrini, B. / Herrmann, T. / Mohanty, B. / Geralt, M. / Wilson, I. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG)
CitationJournal: J.Biomol.Nmr / Year: 2012
Title: The J-UNIO protocol for automated protein structure determination by NMR in solution.
Authors: Serrano, P. / Pedrini, B. / Mohanty, B. / Geralt, M. / Herrmann, T. / Wuthrich, K.
History
DepositionOct 31, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 20, 2012Group: Database references
Revision 1.3Jan 9, 2013Group: Database references
Revision 1.4Feb 19, 2020Group: Data collection / Other / Category: pdbx_database_status / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model
Revision 1.5Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.6May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycine cleavage system H protein


Theoretical massNumber of molelcules
Total (without water)13,9301
Polymers13,9301
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)20 / 80target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Glycine cleavage system H protein


Mass: 13929.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Species: maritima / Gene: gcvH, TM_0212 / Plasmid: pET 25b / Species (production host): coli / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WY55

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1116D APSY HNCOCANH
1215D APSY (HA)CA(CO)NH
1315D APSY CBCA(CO)NH
1413D 1H-15N NOESY
1513D 1H-13C aliphatic NOESY
1613D 1H-13C aromatic NOESY

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Sample preparation

DetailsContents: 2.4 mM [U-100% 13C; U-100% 15N] TM0212, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 2.4 mM / Component: TM0212 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionspH: 6 / Pressure: ambient / Temperature: 313.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
GAPROHiller and Fioritoautomated analysis of 2d apsy nmr projection
MATCHVolk and Herrmannautomated backbone assignment
ASCANFiorito and Herrmannnoesy-based sidechain assignment
ATNOS/CANDIDHerrmann and Guntertpeak picking
ATNOS/CANDIDHerrmann and Guntertpeak assignment and constraint collection
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
OPALpLuginbuhl, Guntert, Billeter and Wuthrichrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 2488 / NOE intraresidue total count: 559 / NOE long range total count: 880 / NOE medium range total count: 405 / NOE sequential total count: 644
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 80 / Conformers submitted total number: 20

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