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- PDB-1ff3: STRUCTURE OF THE PEPTIDE METHIONINE SULFOXIDE REDUCTASE FROM ESCH... -

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Basic information

Entry
Database: PDB / ID: 1ff3
TitleSTRUCTURE OF THE PEPTIDE METHIONINE SULFOXIDE REDUCTASE FROM ESCHERICHIA COLI
ComponentsPEPTIDE METHIONINE SULFOXIDE REDUCTASE
KeywordsOXIDOREDUCTASE / peptide methionine sulfoxide reductase / alpha beta roll / pmsr / msra
Function / homology
Function and homology information


L-methionine-(S)-S-oxide reductase activity / oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor / peptide-methionine (S)-S-oxide reductase / peptide-methionine (S)-S-oxide reductase activity / protein repair / protein modification process / cellular response to oxidative stress / response to oxidative stress / cytoplasm / cytosol
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
Peptide methionine sulfoxide reductase MsrA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsTete-Favier, F. / Cobessi, D. / Boschi-Muller, S. / Azza, S. / Branlant, G. / Aubry, A.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Crystal structure of the Escherichia coli peptide methionine sulphoxide reductase at 1.9 A resolution.
Authors: Tete-Favier, F. / Cobessi, D. / Boschi-Muller, S. / Azza, S. / Branlant, G. / Aubry, A.
History
DepositionJul 25, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PEPTIDE METHIONINE SULFOXIDE REDUCTASE
B: PEPTIDE METHIONINE SULFOXIDE REDUCTASE
C: PEPTIDE METHIONINE SULFOXIDE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3117
Polymers69,9263
Non-polymers3844
Water9,548530
1
A: PEPTIDE METHIONINE SULFOXIDE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5974
Polymers23,3091
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PEPTIDE METHIONINE SULFOXIDE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4052
Polymers23,3091
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PEPTIDE METHIONINE SULFOXIDE REDUCTASE


Theoretical massNumber of molelcules
Total (without water)23,3091
Polymers23,3091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: PEPTIDE METHIONINE SULFOXIDE REDUCTASE

C: PEPTIDE METHIONINE SULFOXIDE REDUCTASE

A: PEPTIDE METHIONINE SULFOXIDE REDUCTASE
B: PEPTIDE METHIONINE SULFOXIDE REDUCTASE
hetero molecules

A: PEPTIDE METHIONINE SULFOXIDE REDUCTASE
B: PEPTIDE METHIONINE SULFOXIDE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,62114
Polymers139,8536
Non-polymers7698
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation5_665y+1,-x+y+1,z+1/61
crystal symmetry operation8_555x-y,-y,-z1
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area6910 Å2
ΔGint-144 kcal/mol
Surface area50300 Å2
MethodPISA
5
A: PEPTIDE METHIONINE SULFOXIDE REDUCTASE
B: PEPTIDE METHIONINE SULFOXIDE REDUCTASE
hetero molecules

A: PEPTIDE METHIONINE SULFOXIDE REDUCTASE
B: PEPTIDE METHIONINE SULFOXIDE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,00412
Polymers93,2354
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area4190 Å2
ΔGint-120 kcal/mol
Surface area35500 Å2
MethodPISA
6
A: PEPTIDE METHIONINE SULFOXIDE REDUCTASE
hetero molecules

C: PEPTIDE METHIONINE SULFOXIDE REDUCTASE


Theoretical massNumber of molelcules
Total (without water)46,9065
Polymers46,6182
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area1830 Å2
ΔGint-50 kcal/mol
Surface area17360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.5, 102.5, 292.3
Angle α, β, γ (deg.)90, 90, 120
Int Tables number179
Space group name H-MP6522
Details: The biological assembly is a monomer

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Components

#1: Protein PEPTIDE METHIONINE SULFOXIDE REDUCTASE / PEPTIDE MET(O) REDUCTASE


Mass: 23308.770 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A744
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / 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: 3.17 Å3/Da / Density % sol: 61.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.35 M ammonium sulphate, 20 % PEG 8K, Cacodylate buffer 0.1 M, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Details: Tete-Favier, F., (2000) Acta Crystallogr. D56, 1194.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mg/mlprotein1drop
220 %PEG80001reservoir
30.35 Mammonium sulfate1reservoir
4100 mMcacodylate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 29, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 64402 / % possible obs: 88.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 21
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.235 / % possible all: 65.6
Reflection
*PLUS
Num. measured all: 291810
Reflection shell
*PLUS
% possible obs: 65.6 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→30 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflectionSelection details
Rfree0.218 6375 RANDOM
Rwork0.195 --
obs-63115 -
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4603 0 20 530 5153
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.326
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.33
LS refinement shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.97 Å / Rfactor Rfree: 0.246 / Num. reflection Rfree: 445 / Rfactor Rwork: 0.214 / Num. reflection Rwork: 3896

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