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Yorodumi- PDB-4mn7: Structural and biochemical analysis of type II free methionine-R-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mn7 | ||||||
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Title | Structural and biochemical analysis of type II free methionine-R-sulfoxide reductase from Thermoplasma acidophilum | ||||||
Components | Putative uncharacterized protein Ta0848 | ||||||
Keywords | OXIDOREDUCTASE / reductase | ||||||
Function / homology | GAF domain / GAF domain / GAF domain / GAF-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta / METHIONINE SULFOXIDE / GAF domain-containing protein Function and homology information | ||||||
Biological species | Thermoplasma acidophilum (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Kim, H.S. / Kwak, G.H. / Lee, K.T. / Jo, C.H. / Hwang, K.Y. / Kim, H.Y. | ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2014 Title: Structural and biochemical analysis of a type II free methionine-R-sulfoxide reductase from Thermoplasma acidophilum Authors: Kim, H.S. / Kwak, G.H. / Lee, K. / Jo, C.H. / Hwang, K.Y. / Kim, H.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mn7.cif.gz | 73.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mn7.ent.gz | 55.3 KB | Display | PDB format |
PDBx/mmJSON format | 4mn7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mn/4mn7 ftp://data.pdbj.org/pub/pdb/validation_reports/mn/4mn7 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16998.279 Da / Num. of mol.: 2 / Mutation: C84S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) Strain: ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165 Gene: Ta0848 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HJW5 #2: Chemical | ChemComp-SME / | #3: 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: 3.55 Å3/Da / Density % sol: 65.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 60%(v/v) tacsimate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97251 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 4, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97251 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 33454 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 40.963 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 2.719 / Rsym value: 0.449 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.83 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.856 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.999 Å2
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Refinement step | Cycle: LAST / Resolution: 2→29.83 Å
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Refine LS restraints |
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