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- PDB-7cto: Staphylococcus aureus MsrB -

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Basic information

Entry
Database: PDB / ID: 7cto
TitleStaphylococcus aureus MsrB
ComponentsPeptide methionine sulfoxide reductase MsrB
KeywordsOXIDOREDUCTASE / methionine sulfoxide reductase
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
Similarity search - Function
Peptide methionine sulfoxide reductase MsrB / Peptide methionine sulphoxide reductase MrsB domain / SelR domain / Methionine-R-sulfoxide reductase (MsrB) domain profile. / Mss4-like superfamily
Similarity search - Domain/homology
Peptide methionine sulfoxide reductase MsrB
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.47 Å
AuthorsKim, H.J.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Implication of Staphylococcus aureus MsrB dimerization upon oxidation.
Authors: Kim, H.J.
History
DepositionAug 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptide methionine sulfoxide reductase MsrB
B: Peptide methionine sulfoxide reductase MsrB
C: Peptide methionine sulfoxide reductase MsrB
D: Peptide methionine sulfoxide reductase MsrB
E: Peptide methionine sulfoxide reductase MsrB
F: Peptide methionine sulfoxide reductase MsrB


Theoretical massNumber of molelcules
Total (without water)109,9466
Polymers109,9466
Non-polymers00
Water00
1
A: Peptide methionine sulfoxide reductase MsrB


Theoretical massNumber of molelcules
Total (without water)18,3241
Polymers18,3241
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptide methionine sulfoxide reductase MsrB


Theoretical massNumber of molelcules
Total (without water)18,3241
Polymers18,3241
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Peptide methionine sulfoxide reductase MsrB


Theoretical massNumber of molelcules
Total (without water)18,3241
Polymers18,3241
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Peptide methionine sulfoxide reductase MsrB


Theoretical massNumber of molelcules
Total (without water)18,3241
Polymers18,3241
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Peptide methionine sulfoxide reductase MsrB


Theoretical massNumber of molelcules
Total (without water)18,3241
Polymers18,3241
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Peptide methionine sulfoxide reductase MsrB


Theoretical massNumber of molelcules
Total (without water)18,3241
Polymers18,3241
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.825, 122.190, 73.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 18324.342 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: msrB, BN1321_260062, C7P97_04695, CSC87_09070, DDL17_13745, DQV20_10340, E3A28_01365, E3K14_07190, ERS072840_01728, FVP29_01290, GF545_14165, GIX97_03240, GO677_01280, GO706_07960, GO793_06600, ...Gene: msrB, BN1321_260062, C7P97_04695, CSC87_09070, DDL17_13745, DQV20_10340, E3A28_01365, E3K14_07190, ERS072840_01728, FVP29_01290, GF545_14165, GIX97_03240, GO677_01280, GO706_07960, GO793_06600, GO810_04540, GO915_14110, GO941_13080, M1K003_0267, NCTC7878_02957, SAMEA1469856_01218, SAMEA1469884_01806, SAMEA1531680_00578, SAMEA1531701_01923, SAST44_01500, SAST45_01536
Production host: Escherichia coli (E. coli)
References: UniProt: W8TTH3, peptide-methionine (R)-S-oxide reductase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% (w/v) PEG 8K, 3% MPD, and 0.1 M Imidazole (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.47→83.68 Å / Num. obs: 13922 / % possible obs: 100 % / Redundancy: 27 % / CC1/2: 1 / Rmerge(I) obs: 0.095 / Net I/σ(I): 32
Reflection shellResolution: 3.47→3.8 Å / Rmerge(I) obs: 0.508 / Num. unique obs: 3257 / CC1/2: 0.967

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
Aimlessdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3E0O

3e0o


Resolution: 3.47→83.68 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.836 / SU B: 40.394 / SU ML: 0.616 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.805 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3233 686 4.9 %RANDOM
Rwork0.2165 ---
obs0.2216 13226 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 247.36 Å2 / Biso mean: 110.997 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2---0.44 Å20 Å2
3---0.73 Å2
Refinement stepCycle: final / Resolution: 3.47→83.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6591 0 0 0 6591
Num. residues----816
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0136763
X-RAY DIFFRACTIONr_bond_other_d0.0020.0175895
X-RAY DIFFRACTIONr_angle_refined_deg1.6751.649132
X-RAY DIFFRACTIONr_angle_other_deg1.1491.5813824
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.7155813
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.25324.582371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.317151155
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8931518
X-RAY DIFFRACTIONr_chiral_restr0.0640.2843
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027628
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021398
LS refinement shellResolution: 3.47→3.557 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.382 52 -
Rwork0.307 946 -
obs--99.8 %

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