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- PDB-1fva: CRYSTAL STRUCTURE OF BOVINE METHIONINE SULFOXIDE REDUCTASE -

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Basic information

Entry
Database: PDB / ID: 1fva
TitleCRYSTAL STRUCTURE OF BOVINE METHIONINE SULFOXIDE REDUCTASE
ComponentsPEPTIDE METHIONINE SULFOXIDE REDUCTASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


Protein repair / L-methionine-(S)-S-oxide reductase activity / peptide-methionine (S)-S-oxide reductase / peptide-methionine (S)-S-oxide reductase activity / cellular response to oxidative stress / mitochondrion / cytoplasm
Similarity search - Function
Peptide Methionine Sulfoxide Reductase; Chain A / Peptide methionine sulphoxide reductase MsrA / : / Peptide methionine sulphoxide reductase MsrA domain / Peptide methionine sulphoxide reductase MsrA superfamily / Peptide methionine sulfoxide reductase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Mitochondrial peptide methionine sulfoxide reductase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLowther, W.T. / Brot, N. / Weissbach, H. / Matthews, B.W.
Citation
Journal: Biochemistry / Year: 2000
Title: Structure and mechanism of peptide methionine sulfoxide reductase, an "anti-oxidation" enzyme.
Authors: Lowther, W.T. / Brot, N. / Weissbach, H. / Matthews, B.W.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Thiol-disulfide Exchange is Involved in the Catalytic Mechanism of Peptide Methionine Sulfoxide Reductase
Authors: Lowther, W.T. / Brot, N. / Weissbach, H. / Honek, J.F. / Matthews, B.W.
History
DepositionSep 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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

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Assembly

Deposited unit
A: PEPTIDE METHIONINE SULFOXIDE REDUCTASE
B: PEPTIDE METHIONINE SULFOXIDE REDUCTASE


Theoretical massNumber of molelcules
Total (without water)48,0662
Polymers48,0662
Non-polymers00
Water3,171176
1
A: PEPTIDE METHIONINE SULFOXIDE REDUCTASE


Theoretical massNumber of molelcules
Total (without water)24,0331
Polymers24,0331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PEPTIDE METHIONINE SULFOXIDE REDUCTASE


Theoretical massNumber of molelcules
Total (without water)24,0331
Polymers24,0331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.710, 66.199, 62.137
Angle α, β, γ (deg.)90.00, 90.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PEPTIDE METHIONINE SULFOXIDE REDUCTASE


Mass: 24032.904 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Plasmid: PET28B / Production host: Escherichia coli (E. coli) / References: UniProt: P54149, EC: 1.8.4.6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 46.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.7
Details: NaCl, DTT, 1,4 butanediol, PEG 8000, citrate, Na2HPO4, pH 4.7-7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.4 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
112 mg/mlprotein1drop
230 mMdithiothreitol1drop
316 mMHEPES1drop
416 mM1dropNaCl
50.08 mMEDTA1drop
65 %1,4-butanediol1drop
7100 mMcitrate1reservoircan be replaced by sodium phosphate
821-25 %PEG80001reservoir
9100 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 21, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→45.2 Å / Num. all: 158892 / Num. obs: 46997 / % possible obs: 97.7 % / Observed criterion σ(I): 3.5 / Redundancy: 3.4 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 35.7
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.225 / % possible all: 84
Reflection
*PLUS
Num. measured all: 158892
Reflection shell
*PLUS
% possible obs: 84 % / Mean I/σ(I) obs: 3.5

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5Erefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1fvg

1fvg


Resolution: 1.7→45.2 Å / σ(I): 3.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.28 4639 random 10%
Rwork0.207 --
all-46997 -
obs-46980 -
Solvent computationBsol: 194.6 Å2 / ksol: 1.003 e/Å3
Refinement stepCycle: LAST / Resolution: 1.7→45.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3138 0 0 176 3314
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01132320.8
X-RAY DIFFRACTIONt_angle_deg2.1843591.3
X-RAY DIFFRACTIONt_dihedral_angle_d18.1918630
X-RAY DIFFRACTIONt_trig_c_planes0.007782
X-RAY DIFFRACTIONt_gen_planes0.0114795
X-RAY DIFFRACTIONt_nbd0.0174810
X-RAY DIFFRACTIONt_incorr_chiral_ct0
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / % reflection Rfree: 10 % / Rfactor obs: 0.207 / Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeWeightDev ideal
X-RAY DIFFRACTIONt_bond_d0.8
X-RAY DIFFRACTIONt_angle_deg1.3
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg018.19
X-RAY DIFFRACTIONt_planar_d20.007
X-RAY DIFFRACTIONt_plane_restr50.011

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