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- PDB-2gbs: NMR structure of Rpa0253 from Rhodopseudomonas palustris. Northea... -

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Basic information

Entry
Database: PDB / ID: 2gbs
TitleNMR structure of Rpa0253 from Rhodopseudomonas palustris. Northeast structural genomics consortium target RpR3
ComponentsHypothetical protein Rpa0253
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta / RpR3 / NESG / Rpa0253 / COG2947 / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


: / : / EVE domain / EVE domain / ph1033 like fold / ph1033 like domains / PUA-like superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodSOLUTION NMR / distance geometry, simulated annealing, torsion angle dynamics, cns water refinement
AuthorsRamelot, T.A. / Cort, J.R. / Conover, K. / Chen, Y. / Ma, L.C. / Ciano, M. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proteins / Year: 2009
Title: Structural genomics reveals EVE as a new ASCH/PUA-related domain.
Authors: Bertonati, C. / Punta, M. / Fischer, M. / Yachdav, G. / Forouhar, F. / Zhou, W. / Kuzin, A.P. / Seetharaman, J. / Abashidze, M. / Ramelot, T.A. / Kennedy, M.A. / Cort, J.R. / Belachew, A. / ...Authors: Bertonati, C. / Punta, M. / Fischer, M. / Yachdav, G. / Forouhar, F. / Zhou, W. / Kuzin, A.P. / Seetharaman, J. / Abashidze, M. / Ramelot, T.A. / Kennedy, M.A. / Cort, J.R. / Belachew, A. / Hunt, J.F. / Tong, L. / Montelione, G.T. / Rost, B.
History
DepositionMar 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 20, 2021Group: Data collection / Database references
Category: database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein Rpa0253


Theoretical massNumber of molelcules
Total (without water)16,2851
Polymers16,2851
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 / 20all calculated structures submitted
RepresentativeModel #1closest to the average

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Components

#1: Protein Hypothetical protein Rpa0253


Mass: 16284.735 Da / Num. of mol.: 1 / Mutation: M1V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: CGA009 / Gene: rpa0253 / Production host: Escherichia coli (E. coli) / Strain (production host): XL-Gold+pMGK / References: UniProt: Q6ND56

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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
1314D 13C-separated NOESY
141HNHA

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Sample preparation

DetailsContents: 1 mM Rpa0253, U-15N, 13C; 20mM MES, 100mM NaCl, 5mM CaCl2, 10 mM DTT, 0.02% NaN3; 95% H2O, 5% D2O, pH 6.5
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 100mM NaCL / pH: 6.5 / Pressure: ambient / 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
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3.1T.D. Goddard and D.G. Knellerdata analysis
NMRPipeLinux9F. Delaglio, A. Baxprocessing
AutoStructure2.1.1Y.J. Huang, G.T. Montelionedata analysis
X-PLORxplor-nih-2.10C.D. Schwieters, J.J. Kuszewski, N. Tjandra, G.M. Clorestructure solution
CNS1.1A. Brunger, G.L. Warrenrefinement
VNMR6.1cVariancollection
RefinementMethod: distance geometry, simulated annealing, torsion angle dynamics, cns water refinement
Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1690 RESTRAINTS. 1512 are NOE-DERIVED; SEQUENTIAL [(I-J)=1] = 201; MEDIUM RANGE [10.1 ANG = 0; AVERAGE RMS DISTANCE VIOLATION / CONSTRAINT = 0.001 ANG.; ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1690 RESTRAINTS. 1512 are NOE-DERIVED; SEQUENTIAL [(I-J)=1] = 201; MEDIUM RANGE [1<(I-J)<5] = 411; LONG RANGE [(I-J)>=5] = 900; HYDROGEN BOND RESTRAINTS = 80 (2 PER H-BOND); NUMBER OF NOE RESTRAINTS PER RESIDUE = 11.0 (RESIDES 2-138); DIHEDRAL-ANGLE RESTRAINTS = 178 (89 PHI, 89 PSI); TOTAL NUMBER OF RESTRAINTS PER RESIDUE = 12.2 (RESIDES 1-138); NUMBER OF LONG RANGE RESTRAINTS PER RESIDUE = 6.5; NUMBER OF STRUCTURES COMPUTED = 20; NUMBER OF STRUCTURES USED = 20. AVERAGE DISTANCE VIOLATIONS >0.1 ANG = 0; AVERAGE RMS DISTANCE VIOLATION / CONSTRAINT = 0.001 ANG.; MAXIMUM DISTANCE VIOLATION 0.038. AVERAGE DIHEDRAL ANGLE VIOLATIONS: >1 DEG = 0; MAX DIHEDRAL ANGLE VIOLATION = 0.73; AVERAGE RMS ANGLE VIOLATION / CONSTRAINT = 0.03 DEG. RMSD VALUES: BACKBONE ATOMS (N,C,C', RESIDUES 2-136) = 0.57 ANG; ALL HEAVY ATOMS = 0.93 ANG; PROCHECK (RESIDUES 2-136): MOST FAVORED REGIONS = 90%; ADDITIONAL ALLOWED REGIONS = 9%; GENEROUSLY ALLOWED REGIONS = 0%; DISALLOWED REGIONS = 1%. THE 8 RESIDUE C-TERMINAL HIS TAG (LEHHHHHH) WAS INCLUDED IN THE STRUCTURE CALCULATION.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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