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Yorodumi- PDB-1o9i: Crystal structure of the Y42F mutant of manganese catalase from L... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1o9i | ||||||
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Title | Crystal structure of the Y42F mutant of manganese catalase from Lactobacillus plantarum at 1.33A resolution | ||||||
Components | Manganese catalase | ||||||
Keywords | OXIDOREDUCTASE / HEXAMER / DIMANGANESE CATALASE / METALLOENZYME / PREOXIDASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Lactobacillus plantarum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å | ||||||
Authors | Barynin, V.V. / Whittaker, M.M. / Whittaker, J.W. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 2003 Title: Outer Sphere Mutagenesis of Lactobacillus Plantarum Manganese Catalase Disrupts the Cluster Core. Mechanistic Implications. Authors: Whittaker, M.M. / Barynin, V.V. / Igarashi, T. / Whittaker, J.W. #1: Journal: Structure / Year: 2001 Title: Crystal Structure of Manganese Catalase from Lactobacillus Plantarum Authors: Barynin, V.V. / Whittaker, M.M. / Antonyuk, S.V. / Lamzin, V.S. / Harrison, P.M. / Artymiuk, P.J. / Whittaker, J.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o9i.cif.gz | 675.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o9i.ent.gz | 558.4 KB | Display | PDB format |
PDBx/mmJSON format | 1o9i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1o9i_validation.pdf.gz | 405.3 KB | Display | wwPDB validaton report |
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Full document | 1o9i_full_validation.pdf.gz | 414.3 KB | Display | |
Data in XML | 1o9i_validation.xml.gz | 32.5 KB | Display | |
Data in CIF | 1o9i_validation.cif.gz | 55.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/1o9i ftp://data.pdbj.org/pub/pdb/validation_reports/o9/1o9i | HTTPS FTP |
-Related structure data
Related structure data | 1jkvS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 29763.379 Da / Num. of mol.: 6 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Plasmid: PVMG36PSLPA-LPC / Production host: LACTOBACILLUS PLANTARUM (bacteria) / Strain (production host): KAT- L.PLANTARUM (NCDO 1193) / References: UniProt: P60355, catalase |
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-Non-polymers , 6 types, 1490 molecules
#2: Chemical | ChemComp-MN3 / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-O / #5: Chemical | ChemComp-MES / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED |
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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: 1.97 Å3/Da / Density % sol: 37.66 % | ||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 8000, TAPS, PH 8.5, VAPOR DIFFUSION, HANGING DROP AT 291K | ||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 8.7 / Method: vapor diffusion | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 9, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→50 Å / Num. obs: 282601 / % possible obs: 86.7 % / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Biso Wilson estimate: 14.28 Å2 / Rsym value: 0.041 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.33→1.35 Å / Redundancy: 1.88 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.34 / % possible all: 80.7 |
Reflection | *PLUS Highest resolution: 1.33 Å / Lowest resolution: 23 Å / Num. obs: 274725 / Redundancy: 2.14 % / Num. measured all: 588079 / Rmerge(I) obs: 0.041 |
Reflection shell | *PLUS % possible obs: 80.7 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 1.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JKV Resolution: 1.33→50 Å / SU B: 2.092 / SU ML: 0.043 / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.047 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Displacement parameters | Biso mean: 16.33 Å2
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Refinement step | Cycle: LAST / Resolution: 1.33→50 Å
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Refinement | *PLUS Lowest resolution: 48 Å / % reflection Rfree: 5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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