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Yorodumi- PDB-3mmh: X-ray structure of free methionine-R-sulfoxide reductase from nei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mmh | ||||||
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Title | X-ray structure of free methionine-R-sulfoxide reductase from neisseria meningitidis in complex with its substrate | ||||||
Components | Methionine-R-sulfoxide reductase | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | GAF domain / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta / ACETATE ION / METHIONINE SULFOXIDE / : Function and homology information | ||||||
Biological species | Neisseria meningitidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å | ||||||
Authors | Gruez, A. / Libiad, M. / Boschi-Muller, S. / Branlant, G. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mmh.cif.gz | 158.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mmh.ent.gz | 132.4 KB | Display | PDB format |
PDBx/mmJSON format | 3mmh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mmh_validation.pdf.gz | 481.9 KB | Display | wwPDB validaton report |
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Full document | 3mmh_full_validation.pdf.gz | 487.6 KB | Display | |
Data in XML | 3mmh_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 3mmh_validation.cif.gz | 28.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mm/3mmh ftp://data.pdbj.org/pub/pdb/validation_reports/mm/3mmh | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | DIMER |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | 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 | #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-MRD / ( #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.92 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.886 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 23, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.886 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 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 |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 96.46 Å2 / Biso mean: 19.68 Å2 / Biso min: 5.69 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.25→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.25→1.282 Å / Total num. of bins used: 20
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