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- PDB-1fvg: CRYSTAL STRUCTURE OF BOVINE PEPTIDE METHIONINE SULFOXIDE REDUCTASE -

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Basic information

Entry
Database: PDB / ID: 1fvg
TitleCRYSTAL STRUCTURE OF BOVINE PEPTIDE 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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Mitochondrial peptide methionine sulfoxide reductase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 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 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PEPTIDE METHIONINE SULFOXIDE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5402
Polymers22,3851
Non-polymers1541
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.757, 76.883, 56.745
Angle α, β, γ (deg.)90.00, 109.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PEPTIDE METHIONINE SULFOXIDE REDUCTASE


Mass: 22385.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DITHIOTHREITOL COMPLEX / Source: (gene. exp.) Bos taurus (domestic cattle) / Plasmid: PET28B / Production host: Escherichia coli (E. coli) / References: UniProt: P54149, EC: 1.8.4.6
#2: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 41.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: dithiothreitol, PEG 8000, citrate, Na2HPO4, dimethyl sulfoxide, NaCl, pH 4.70, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
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
66 %DMSO1drop
7100 mMcitrate1reservoircan be replaced by sodium phosphate
826-31 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9787,0.9788,0.9537
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 21, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97871
20.97881
30.95371
ReflectionResolution: 1.6→53.5 Å / Num. all: 86018 / Num. obs: 23472 / % possible obs: 95.8 % / Observed criterion σ(I): 8 / Redundancy: 4 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 37.2
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4 % / Rmerge(I) obs: 0.171 / % possible all: 93.9
Reflection
*PLUS
Num. measured all: 86018
Reflection shell
*PLUS
% possible obs: 93.9 % / Mean I/σ(I) obs: 8

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Processing

Software
NameVersionClassification
SHARPphasing
TNT5Erefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.6→53.58 Å / σ(I): 8 / Stereochemistry target values: Engh & Huber
Details: The structure factors represent the "optimized" reference structure factors (Fpsha) from a three wavelength MAD experiment analyzed by SHARP.
RfactorNum. reflectionSelection details
Rfree0.242 2334 random 10%
Rwork0.182 --
obs-23882 -
Solvent computationBsol: 141.2 Å2 / ksol: 0.802 e/Å3
Refinement stepCycle: LAST / Resolution: 1.6→53.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1525 0 8 140 1673
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0115800.8
X-RAY DIFFRACTIONt_angle_deg2.1321301.3
X-RAY DIFFRACTIONt_dihedral_angle_d15.9249140
X-RAY DIFFRACTIONt_trig_c_planes0.007192
X-RAY DIFFRACTIONt_gen_planes0.0122315
X-RAY DIFFRACTIONt_nbd0.0341610
X-RAY DIFFRACTIONt_incorr_chiral_ct0
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / % reflection Rfree: 10 % / Rfactor obs: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeWeightDev ideal
X-RAY DIFFRACTIONt_angle_deg1.3
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg015.924
X-RAY DIFFRACTIONt_planar_d20.007
X-RAY DIFFRACTIONt_plane_restr50.012

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