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Yorodumi- PDB-2kzn: Solution NMR Structure of Peptide methionine sulfoxide reductase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kzn | |||||||||
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Title | Solution NMR Structure of Peptide methionine sulfoxide reductase msrB from Bacillus subtilis, Northeast Structural Genomics Consortium Target SR10 | |||||||||
Components | Peptide methionine sulfoxide reductase msrB | |||||||||
Keywords | OXIDOREDUCTASE / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / Protein Structure Initiative / PSI-2 | |||||||||
Function / homology | Function and homology information peptide-methionine (R)-S-oxide reductase / peptide-methionine (R)-S-oxide reductase activity / protein repair / response to oxidative stress / cytoplasm Similarity search - Function | |||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||
Method | SOLUTION NMR / molecular dynamics | |||||||||
Model details | lowest energy, model 1 | |||||||||
Authors | Ertekin, A. / Maglaqui, M. / Janjua, H. / Cooper, B. / Ciccosanti, C. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Prestegard, J. ...Ertekin, A. / Maglaqui, M. / Janjua, H. / Cooper, B. / Ciccosanti, C. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Prestegard, J. / Lee, H. / Aramini, J.M. / Rossi, P. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples. Authors: Lange, O.F. / Rossi, P. / Sgourakis, N.G. / Song, Y. / Lee, H.W. / Aramini, J.M. / Ertekin, A. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Baker, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kzn.cif.gz | 915 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kzn.ent.gz | 768.7 KB | Display | PDB format |
PDBx/mmJSON format | 2kzn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2kzn_validation.pdf.gz | 344.1 KB | Display | wwPDB validaton report |
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Full document | 2kzn_full_validation.pdf.gz | 472 KB | Display | |
Data in XML | 2kzn_validation.xml.gz | 55.2 KB | Display | |
Data in CIF | 2kzn_validation.cif.gz | 75 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kz/2kzn ftp://data.pdbj.org/pub/pdb/validation_reports/kz/2kzn | HTTPS FTP |
-Related structure data
Related structure data | 2kw5C 2lmdC 2lnuC 2lokC 2loyC 2mv0C C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 17697.691 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU21680, msrB, yppQ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK References: UniProt: P54155, peptide-methionine (R)-S-oxide reductase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: MONOMER BY GEL FILTRATION CHROMATOGRAPHY/LIGHT SCATTERING AND BY NMR.T1/T2(CPMG) (MS/MS) = 921/57 AT 800MHz, TAUC = 9.3(NS). CONSISTENT WITH MOLECULAR WEIGHT. |
-Sample preparation
Details |
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Sample |
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Sample conditions | pH: 6.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 1 Details: STRUCTURE DETERMINED BY SPARSE CONSTRAINTS FROM UNIFORMLY DEUTERATED, METHYL BACK-PROTONATED(ILE,VAL,LEU). NOESY ASSIGNMENTS BY CYANA-3.0 WITH RDC. 20 OF 100 STRUCTURES LOWEST TARGET ...Details: STRUCTURE DETERMINED BY SPARSE CONSTRAINTS FROM UNIFORMLY DEUTERATED, METHYL BACK-PROTONATED(ILE,VAL,LEU). NOESY ASSIGNMENTS BY CYANA-3.0 WITH RDC. 20 OF 100 STRUCTURES LOWEST TARGET FUNCTION SELECTED WITH CYANA-3.0. SELECTED MODELS ARE FURTHER REFINED USING CNS IN EXPLICIT WATER SHELL AND RDC SAMPLE ALIGNED IN PHAGE (NILGES PROTOCOL WITH PARAM19). ASSIGNMENT STATS (ALL RESIDUES INCLUDED): BACKBONE 72.96%, SIDECHAIN 21.00%, AROMATIC (SC) 00.00%, STEREOSPECIFIC VL METHYL ASSIGNMENT 100%, UNAMBIGUOUS SIDECHAIN NH2 57.14%. STRUCTURE BASED ON 603 NOE, 235 DIHE, 85 RDC. MAX NOE VIOLATION: 1.85 A; MAX DIHE VIOLATION: 20.7 DEG. 50 TOTAL CLOSE CONTACTS PER 20 MODELS. STRUCTURE QUALITY FACTOR (PSVS 1.3): ORDERED RESIDUES RANGES: 4-27, 31-33, 37-59, 64-80, 84-95, 98-133, 134-141 FOR [S(PHI)+S(PSI)] > 1.8. SECONDARY STRUCTURE - ALPHA HELICES: 5-22, 126-132, 134-141; BETA STRANDS: 49-53, 40-44, 121-125, 66-67, 113-116, 100-103, 86-90, 77-81 RMSD(ANG): BACKBONE 2.1, ALL -0.45/-1.46 (RAW/Z), PROCHECK (ALL): -0.38/-2.25 (RAW/Z), MOLPROBITY CLASH: 18.61/-1.67 (RAW/Z). RDC STATISTICS FROM CYANA-3.0. DA = -5.404 HZ, RHOM = 0.48; CORR. COEFF: 0.919 +/- 0.012, Q-FACTOR: 25.162 +/- 1.869%. AFTER CNS WATER REFINEMENT WITH RDC PALES COMPUTED CORR. COEFF: 0.976 AND Q-FACTOR: 14.0%. | ||||||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |