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- PDB-3hcj: Structure of MsrB from Xanthomonas campestris (oxidized form) -

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Basic information

Entry
Database: PDB / ID: 3hcj
TitleStructure of MsrB from Xanthomonas campestris (oxidized form)
ComponentsPeptide methionine sulfoxide reductase
KeywordsOXIDOREDUCTASE / Methionine sulfoxide reductase B / Xanthomonas campestris / oxidized form
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 / zinc ion binding / 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 / Peptide methionine sulfoxide reductase MsrB
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.66 Å
AuthorsRanaivoson, F.M. / Kauffmann, B. / Favier, F.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Methionine Sulfoxide Reductase B Displays a High Level of Flexibility.
Authors: Ranaivoson, F.M. / Neiers, F. / Kauffmann, B. / Boschi-Muller, S. / Branlant, G. / Favier, F.
History
DepositionMay 6, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8434
Polymers33,7122
Non-polymers1312
Water8,143452
1
A: Peptide methionine sulfoxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9212
Polymers16,8561
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptide methionine sulfoxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9212
Polymers16,8561
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.197, 65.303, 57.957
Angle α, β, γ (deg.)90.000, 94.810, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Peptide methionine sulfoxide reductase / MsrB


Mass: 16855.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Gene: msrb, xcc-b100_3837 / Plasmid: pSKMsrBXc / Production host: Escherichia coli (E. coli) / Strain (production host): BE002
References: UniProt: B0RWG5, UniProt: Q8P4Q6*PLUS, peptide-methionine (S)-S-oxide reductase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 452 / 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: 2.47 Å3/Da / Density % sol: 50.25 %
Crystal growTemperature: 293 K / Method: microbatch under oil / pH: 8.5
Details: 32 % PEG 4000, 0.8M LiCl, 0.1M TRIS-HCl pH 8.5, TRIS HCl pH 8, microbatch under oil, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X11 / Wavelength: 0.81 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2004
RadiationMonochromator: Triangular / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 1.66→50 Å / Num. all: 38869 / Num. obs: 38713 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rsym value: 0.038 / Net I/σ(I): 24.1
Reflection shellResolution: 1.66→1.72 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.37 / % possible all: 97.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0066refinement
PDB_EXTRACT3.006data extraction
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
RefinementResolution: 1.66→43.27 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.917 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUE: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1925 5 %RANDOM
Rwork0.201 ---
all0.203 38736 --
obs0.203 38391 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 58.17 Å2 / Biso mean: 23.174 Å2 / Biso min: 10.01 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.66→43.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 2 452 2886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212514
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.9663442
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9415321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.55623.033122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7315363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8991523
X-RAY DIFFRACTIONr_chiral_restr0.0940.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0222048
X-RAY DIFFRACTIONr_mcbond_it0.8251.51589
X-RAY DIFFRACTIONr_mcangle_it1.44422576
X-RAY DIFFRACTIONr_scbond_it2.0953925
X-RAY DIFFRACTIONr_scangle_it3.274.5866
LS refinement shellResolution: 1.662→1.705 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 148 -
Rwork0.244 2573 -
all-2721 -
obs-2721 94.74 %

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