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

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Basic information

Entry
Database: PDB / ID: 1yez
TitleSolution structure of the conserved protein from the gene locus MM1357 of Methanosarcina mazei. Northeast Structural Genomics target MaR30.
ComponentsMM1357
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / MaR30 / Autostructure / Northeast Structural Genomics / 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 / Conserved protein
Function and homology information
Biological speciesMethanosarcina mazei (archaea)
MethodSOLUTION NMR
AuthorsRossi, P. / Aramini, J.M. / Swapna, G.V.T. / Huang, Y.P. / Xiao, R. / Ho, C.K. / Ma, L.C. / Acton, T.B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution structure of the conserved protein from the gene locus MM1357 of Methanosarcina mazei. Northeast Structural Genomics target MaR30.
Authors: Rossi, P. / Aramini, J.M. / Swapna, G.V.T. / Huang, Y.P. / Xiao, R. / Ho, C.K. / Ma, L.C. / Acton, T.B. / Montelione, G.T.
History
DepositionDec 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
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: MM1357


Theoretical massNumber of molelcules
Total (without water)7,6211
Polymers7,6211
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 MM1357


Mass: 7620.669 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea) / Strain: Go1 / Gene: Locus MM1357 / Plasmid: MaR30-21.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21MGK / References: UniProt: Q8PX65

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
1323D 13C-separated NOESY
142Hi-res CH-HSQC, (H)CCH-COSY
153Hi-res CH-HSQC (stereo V and L Meth.), HNHA
161TR exp. backbone, TOCSYs, (H)CCH-COSY
NMR detailsText: CS assign.: Backbone AutoAssign, sidechain HcCH-COSY and TOCSYs. AutoStructure for noesy assign. Hyper Dihedral, Dyana, Xplor(nih), and CNS force-field for simulated annealing and RPF score calculation.

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM MaR30 U-13C,15N, 0.02% NaN3, 10mM DTT, 5mM CaCl2, 100mM NaCl, 20mM MES, 5% D2O/95% H2O5% D2O/95% H2O
20.56mM MaR30 U-13C,15N, 0.02% NaN3, 10mM DTT, 5mM CaCl2, 100mM NaCl, 20mM MES, 100% D2O100% D2O
30.78mM MaR30 U-15N,5% 13C 0.02% NaN3, 10mM DTT, 5mM CaCl2, 100mM NaCl, 20mM MES, 5% D2O/95% H2O5% D2O/95% H2O
Sample conditionsIonic strength: 100 mM NaCl / pH: 6.5 / Pressure: atmospheric atm / Temperature: 293 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
XwinNMR3.5Bruker Biospincollection
NMRPipe2.1Delaglioprocessing
Sparky3.91Goddarddata analysis
AutoAssign1.14Zimmerman,Moseley,Montelionedata analysis
AutoStructure2.1.0Huang,Montelionerefinement
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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