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- PDB-1yvc: Solution structure of the conserved protein from the gene locus M... -

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Basic information

Entry
Database: PDB / ID: 1yvc
TitleSolution structure of the conserved protein from the gene locus MMP0076 of Methanococcus maripaludis. Northeast Structural Genomics target MrR5.
ComponentsMrR5
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / MrR5 / AutoStructure / AutoAssign / Northeast Structural Genomics / AutoQF / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyTRAM domain / TRAM domain / TRAM domain profile. / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta / TRAM domain-containing protein
Function and homology information
Biological speciesMethanococcus maripaludis (archaea)
MethodSOLUTION NMR
AuthorsNortheast Structural Genomics Consortium (NESG) / Rossi, P. / Aramini, J.M. / Xiao, R. / Ho, C.K. / Ma, L.C. / Acton, T.B. / Montelione, G.T.
CitationJournal: To be Published
Authors: Rossi, P. / Aramini, J.M. / Xiao, R. / Ho, C.K. / Ma, L.C. / Acton, T.B. / Montelione, G.T.
History
DepositionFeb 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MrR5


Theoretical massNumber of molelcules
Total (without water)7,5121
Polymers7,5121
Non-polymers00
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 / 56target function
RepresentativeModel #1lowest target function

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Components

#1: Protein MrR5


Mass: 7511.731 Da / Num. of mol.: 1 / Fragment: gene locus MMP0076
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus maripaludis (archaea) / Gene: Locus MMP0076 / Plasmid: MrR5-21.2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21MGK / References: UniProt: Q6M142

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2123D 13C-separated NOESY
2223D 15N-separated NOESY
232(H)CCH-COSY,
141Hi-Res CH-HSQC(st. Me assign), HNHA, HetNOE
252TR backbone, H,C TOCSYs, NH-HSQC
NMR detailsText: CS assign: AutoAssign (bb), HcCH-cosy + TOCSYs (sc), AutoStructure (noe), Hyper (Dihe), Dyana,Xplor,CNS(imp. H2O) (sim. annealing) AutoQF quality factor calc.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.1mM MrR5 U-15N, 5%13C, 10mM DTT, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 0.02% NaN3, pH 4.55% D2O/95% H2O
21.2mM MrR5 U-13C,15N, 10mM DTT, 5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 0.02% NaN3, pH 4.55% D2O/95% H2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 mM NaCl 4.5 atmospheric atm293 K
2100 mM NaCl 4.5 atmospheric atm293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AVANCEBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Variancollection
XwinNMR3.5Bruker Biospincollection
NMRPipe2.1Delaglio (NIH)processing
Sparky3.91Goddard (UCSF)data analysis
AutoAssign1.15.1Zimmerman (Rutgers)data analysis
AutoStructure2.1.0Huang (Rutgers)structure solution
AutoStructure2.1.0Huang (Rutgers)refinement
NMR representativeSelection criteria: lowest target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 56 / Conformers submitted total number: 10

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