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- PDB-2kzn: Solution NMR Structure of Peptide methionine sulfoxide reductase ... -

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Basic information

Entry
Database: PDB / ID: 2kzn
TitleSolution NMR Structure of Peptide methionine sulfoxide reductase msrB from Bacillus subtilis, Northeast Structural Genomics Consortium Target SR10
ComponentsPeptide methionine sulfoxide reductase msrB
KeywordsOXIDOREDUCTASE / 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
Peptide methionine sulfoxide reductase MsrB / Peptide methionine sulphoxide reductase MrsB domain / SelR domain / Methionine-R-sulfoxide reductase (MsrB) domain profile. / Peptide methionine sulfoxide reductase. / Mss4-like superfamily / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Peptide methionine sulfoxide reductase MsrB
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsErtekin, 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)
CitationJournal: 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
DepositionJun 18, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
SupersessionAug 11, 2010ID: 1XM0
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 18, 2012Group: Database references
Revision 1.3Jun 27, 2012Group: Database references
Revision 1.4Jul 18, 2012Group: Database references
Revision 1.5May 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 / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptide methionine sulfoxide reductase msrB


Theoretical massNumber of molelcules
Total (without water)17,6981
Polymers17,6981
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Peptide methionine sulfoxide reductase msrB / Peptide-methionine (R)-S-oxide reductase


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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HNCA
1513D TRHNCACB 2H dec
1613D HN(CA)CO
1712D 1H-15N HSQC - T1
1812D 1H-15N HSQC - T2
1913D 1H-15N NOESY
11013D 1H-13C NOESY
11113D (N15)HSQC-NOESY-(N15)HSQC
11213D (C13)HSQC-NOESY-(C13)HSQC
11313D (N15)HSQC-NOESY-(C13)HSQC
11413D (C13)HSQC-NOESY-(N15)HSQC
11522D 1H-13C HSQC
11632D 1H-15N TROSY
NMR detailsText: 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.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-100% 13C; U-100% 15N; U-100% 2H] SR10, 10 mM DTT, 0.02 % sodium azide, 5 mM calcium chloride, 100 mM sodium chloride, 1 x protease inhibitor, 20 mM MES, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
21.2 mM [U-5% 13C; U-100% 15N] SR10, 10 mM DTT, 0.02 % sodium azide, 5 mM calcium chloride, 100 mM sodium chloride, 1 x protease inhibitor, 20 mM MES, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
31.2 mM [U-5% 13C; U-100% 15N] SR10, 10 mM DTT, 0.02 % sodium azide, 5 mM calcium chloride, 200 mM sodium chloride, 1 x protease inhibitor, 20 mM MES, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMSR10-1[U-100% 13C; U-100% 15N; U-100% 2H]1
10 mMDTT-21
0.02 %sodium azide-31
5 mMcalcium chloride-41
100 mMsodium chloride-51
1 %protease inhibitor-61
20 mMMES-71
50 uMDSS-81
1.2 mMSR10-9[U-5% 13C; U-100% 15N]2
10 mMDTT-102
0.02 %sodium azide-112
5 mMcalcium chloride-122
100 mMsodium chloride-132
1 %protease inhibitor-142
20 mMMES-152
50 uMDSS-162
1.2 mMSR10-17[U-5% 13C; U-100% 15N]3
10 mMDTT-183
0.02 %sodium azide-193
5 mMcalcium chloride-203
200 mMsodium chloride-213
1 %protease inhibitor-223
20 mMMES-233
50 uMDSS-243
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinemen,structure solution,geometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
SparkyGoddarddata analysis
SparkyGoddardpeak picking
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PALESPALES (Zweckstetter, Bax)geometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: 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 representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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