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- PDB-3mmh: X-ray structure of free methionine-R-sulfoxide reductase from nei... -

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Basic information

Entry
Database: PDB / ID: 3mmh
TitleX-ray structure of free methionine-R-sulfoxide reductase from neisseria meningitidis in complex with its substrate
ComponentsMethionine-R-sulfoxide reductase
KeywordsOXIDOREDUCTASE
Function / homologyGAF domain / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta / ACETATE ION / METHIONINE SULFOXIDE / :
Function and homology information
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å
AuthorsGruez, A. / Libiad, M. / Boschi-Muller, S. / Branlant, G.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural and Biochemical Characterization of Free Methionine-R-sulfoxide Reductase from Neisseria meningitidis.
Authors: Gruez, A. / Libiad, M. / Boschi-Muller, S. / Branlant, G.
History
DepositionApr 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2010Provider: 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: Methionine-R-sulfoxide reductase
B: Methionine-R-sulfoxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,50719
Polymers36,3672
Non-polymers1,14017
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-85 kcal/mol
Surface area13940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.320, 39.480, 52.250
Angle α, β, γ (deg.)104.17, 105.16, 100.50
Int Tables number1
Space group name H-MP1
DetailsDIMER

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Methionine-R-sulfoxide reductase / fRMsr


Mass: 18183.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: 8013 / Gene: CAX50842, NMV_2074 / Plasmid: pSK / Production host: Escherichia coli (E. coli) / Strain (production host): HB101
References: UniProt: C9X208, L-methionine (R)-S-oxide reductase

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Non-polymers , 5 types, 323 molecules

#2: Chemical ChemComp-SME / METHIONINE SULFOXIDE / Methionine sulfoxide


Type: L-peptide linking / Mass: 165.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO3S
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.01 Å3/Da / Density % sol: 38.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.25
Details: 23% MPD, 120 mM Mg(CH3COO)2, 100 mM cacodylate, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.886 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 23, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.886 Å / Relative weight: 1
ReflectionResolution: 1.2→25 Å / Num. obs: 75066 / % possible obs: 84.4 % / Observed criterion σ(I): -3 / Redundancy: 8.54 % / Biso Wilson estimate: 18.941 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 19.91
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.2-1.230.4183.18104246537.4
1.23-1.260.3753.510775307948.3
1.26-1.30.2754.713469384661.5
1.3-1.340.2355.317088495382.1
1.34-1.390.2136.320659548593.4
1.39-1.430.1688.120984532393.6
1.43-1.490.1319.920390517194.3
1.49-1.550.112.719669498694.4
1.55-1.620.07715.719004481995.1
1.62-1.70.06418.218086459695
1.7-1.790.10222.625538442695.4
1.79-1.90.0762724335415296
1.9-2.030.05632.122882391396.2
2.03-2.190.04237.721583370796.4
2.19-2.40.03740.719452336497.1
2.4-2.680.03342.817596306296.9
2.68-3.10.03245.115360271897.6
3.1-3.790.02945.312168231197.6
3.79-5.360.025417979174696.6
5.360.02437.9392194493.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å25.76 Å
Translation3.5 Å25.76 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→20 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.973 / WRfactor Rfree: 0.16 / WRfactor Rwork: 0.119 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.926 / SU B: 1.179 / SU ML: 0.024 / SU R Cruickshank DPI: 0.043 / SU Rfree: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.043 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.157 3545 5 %RANDOM
Rwork0.118 ---
obs0.12 70912 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 96.46 Å2 / Biso mean: 19.68 Å2 / Biso min: 5.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20.09 Å20.08 Å2
2---0.03 Å20.01 Å2
3----0.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.057 Å0.128 Å
Luzzati sigma a0.058 Å0.048 Å
Refinement stepCycle: LAST / Resolution: 1.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2564 0 69 306 2939
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222912
X-RAY DIFFRACTIONr_bond_other_d0.0010.021905
X-RAY DIFFRACTIONr_angle_refined_deg2.2861.9714025
X-RAY DIFFRACTIONr_angle_other_deg1.2434671
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4065401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65923.923130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17615446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2031518
X-RAY DIFFRACTIONr_chiral_restr0.2850.2456
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023364
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02614
X-RAY DIFFRACTIONr_mcbond_it2.4881.51811
X-RAY DIFFRACTIONr_mcbond_other0.8651.5724
X-RAY DIFFRACTIONr_mcangle_it3.51622933
X-RAY DIFFRACTIONr_scbond_it5.06531101
X-RAY DIFFRACTIONr_scangle_it6.84.51067
X-RAY DIFFRACTIONr_rigid_bond_restr2.25834817
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 159 -
Rwork0.17 3026 -
all-3185 -
obs--100 %

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