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- PDB-2fvt: NMR Structure of the Rpa2829 protein from Rhodopseudomonas palust... -

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Basic information

Entry
Database: PDB / ID: 2fvt
TitleNMR Structure of the Rpa2829 protein from Rhodopseudomonas palustris: Northeast Structural Genomics Target RpR43
Componentsconserved hypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / MTH938-like fold / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyHypothetical Protein Mth938; Chain: A, / MTH938-like / NDUFAF3/Mth938 domain-containing protein / MTH938-like superfamily / Protein of unknown function (DUF498/DUF598) / 3-Layer(aba) Sandwich / Alpha Beta / : / Mth938-like domain-containing protein
Function and homology information
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodSOLUTION NMR / The initial structure was determined using automated structure determination (AutoStructure), refined manually. A final refinement used simultated annealing in explicit solvent.
AuthorsCort, J.R. / Ho, C.K. / Cunningham, K. / Ma, L.C. / Conover, K. / Xiao, R. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR Structure of the Rpa2829 protein from Rhodopseudomonas palustris
Authors: Cort, J.R. / Ho, C.K. / Cunningham, K. / Ma, L.C. / Conover, K. / Xiao, R. / Montelione, G.T. / Kennedy, M.A.
History
DepositionJan 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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
Remark 999Sequence According to authors,this is a sequencing error or an isoform resulting from a slight ...Sequence According to authors,this is a sequencing error or an isoform resulting from a slight difference in the sequenced strain and the cloning strain.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: conserved hypothetical protein


Theoretical massNumber of molelcules
Total (without water)15,1291
Polymers15,1291
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 / 30structures with lowest energy and fewest restraint violations
RepresentativeModel #1few violations and low energy and good geometery

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Components

#1: Protein conserved hypothetical protein


Mass: 15129.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Gene: Rpa2829 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: GenBank: 39649750, UniProt: Q6N5Y9*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2114D 13C-separated NOESY
1213D 13C-separated NOESY
1313D 15N-separated NOESY
141HNHA

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM Rpa2829 U-15N,13C; 20 mM ammonium acetate pH 5.0; 100 mM NaCl; 5mM CaCl2; 0.02% NaN3; 10 mM DTT; 95% H2O; 10% D2O95% H2O; 10% D2O
21.2 mM Rpa2829 U-15N,13C; 20 mM ammonium acetate pH 5.0; 100 mM NaCl, 5mM CaCl2, 0.02% NaN3; 100% D2O100% D2O
30.8 mM Rpa2829 U-15N,5% fractionally labeled 13C; 20 mM ammonium acetate pH 4.5; 100 mM NaCl, 5mM CaCl2, 0.02% NaN3; 95% H2O; 10% D2O95% H2O; 10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 mM NaCl; 5mM CaCl2; 20 mM Ammonium acetate 5ambient 293 K
2100 mM NaCl; 5mM CaCl2; 20 mM Ammonium acetate 4.5ambient 293 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 INOVAVarianINOVA8001
Varian INOVAVarianINOVA7502
Varian INOVAVarianINOVA6003
Varian UNITYPLUSVarianUNITYPLUS5004

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
Felix98MSI/Accelerysprocessing
Sparky3.106Tom Goddard, Tom Jamesdata analysis
AutoStructure2.1.1Janet Huang, G.T. Montelionestructure solution
X-PLORNIH-XPLORA. Brungerrefinement
CNS1.1A. Brungerrefinement
RefinementMethod: The initial structure was determined using automated structure determination (AutoStructure), refined manually. A final refinement used simultated annealing in explicit solvent.
Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1039 RESTRAINTS. SUMMARY OF EXPERIMENTAL CONSTRAINTS: RESTRAINING DISTANCE RESTRAINTS: TOTAL = 864; INTRA-RESIDUE [I=J] = 160; SEQUENTIAL [(I-J)=1] = ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1039 RESTRAINTS. SUMMARY OF EXPERIMENTAL CONSTRAINTS: RESTRAINING DISTANCE RESTRAINTS: TOTAL = 864; INTRA-RESIDUE [I=J] = 160; SEQUENTIAL [(I-J)=1] = 225; MEDIUM RANGE [1<(I-J)<5] = 131; LONG RANGE [(I-J)>=5] = 348; HYDROGEN BOND RESTRAINTS = 72 (2 PER H-BOND); NUMBER OF RESTRAINING DISTANCE RESTRAINTS PER RESTRAINED RESIDUE = 8.2; DIHEDRAL-ANGLE RESTRAINTS = 103 (50 PHI, 52 PSI, 1 CHI-1); TOTAL NUMBER OF RESTRAINTS PER RESTRAINED RESIDUE = 8.9; NUMBER OF LONG RANGE NOE DISTANCE RESTRAINTS PER RESTRAINED RESIDUE = 3.0; NUMBER OF STRUCTURES COMPUTED = 30; NUMBER OF STRUCTURES USED = 20. AVERAGE DISTANCE VIOLATIONS >0.0001 ANG = 26.8+/-6; AVERAGE R.M.S. DISTANCE VIOLATION = 0.005 +/- 0.001 ANG; MAXIMUM NUMBER OF DISTANCE VIOLATIONS 39.MAXIMUM DISTANCE VIOLATION = 0.26 ANG; AVERAGE DIHEDRAL ANGLE VIOLATIONS: >0.0001 DEG = 3.3+/-1.3; MAX NUMBER OF DIHEDRAL ANGLE VIOLATIONS = 5; AVERAGE R.M.S. ANGLE VIOLATION = 0.42 +/- .01 DEG.; RMSD VALUES: BACKBONE ATOMS (N,C,C' RESIDUES 10-126) = 0.86 ANG, ALL HEAVY ATOMS = 1.52 ANG; BACKBONE ATOMS (N,C,C' RESIDUES 33-126) = 0.68 ANG, ALL HEAVY ATOMS = 1.1.38 ANG; BACKBONE ATOMS (N,C,C' RESIDUES 12-16,24-26,34-39,41-49,52-74,79-92,95-114,119-126) = 0.67 ANG,ALL HEAVY ATOMS = 1.19 ANG; PROCHECK (RESDIUES 10-126): MOST FAVORED REGIONS = 83.8%; ADDITIONAL ALLOWED REGIONS = 14.9%; GENEROUSLY ALLOWED REGIONS = 1.9%; DISALLOWED REGIONS = 0.4%.
NMR representativeSelection criteria: few violations and low energy and good geometery
NMR ensembleConformer selection criteria: structures with lowest energy and fewest restraint violations
Conformers calculated total number: 30 / Conformers submitted total number: 20

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