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Yorodumi- PDB-1m7s: Crystal Structure Analysis of Catalase CatF of Pseudomonas syringae -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m7s | ||||||
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Title | Crystal Structure Analysis of Catalase CatF of Pseudomonas syringae | ||||||
Components | Catalase | ||||||
Keywords | OXIDOREDUCTASE / BETA BARREL / ALPHA HELICAL DOMAIN | ||||||
Function / homology | Function and homology information catalase / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / periplasmic space / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas syringae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Carpena, X. / Soriano, M. / Klotz, M.G. / Duckworth, H.W. / Donald, L.J. / Melik-Adamyan, W. / Fita, I. / Loewen, P.C. | ||||||
Citation | Journal: Proteins / Year: 2003 Title: Structure of the Clade 1 catalase, CatF of Pseudomonas syringae, at 1.8 A resolution Authors: Carpena, X. / Soriano, M. / Klotz, M.G. / Duckworth, H.W. / Donald, L.J. / Melik-Adamyan, W. / Fita, I. / Loewen, P.C. | ||||||
History |
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Remark 999 | SEQUENCE ACCORDING TO THE AUTHOR, THERE WERE ERRORS IN THE ORIGINAL DNA SEQUENCE. THE SEQUENCE ...SEQUENCE ACCORDING TO THE AUTHOR, THERE WERE ERRORS IN THE ORIGINAL DNA SEQUENCE. THE SEQUENCE PRESENTED IN THE ENTRY IS CORRECT. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m7s.cif.gz | 434.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m7s.ent.gz | 350.1 KB | Display | PDB format |
PDBx/mmJSON format | 1m7s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m7s_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 1m7s_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 1m7s_validation.xml.gz | 93.8 KB | Display | |
Data in CIF | 1m7s_validation.cif.gz | 140.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m7/1m7s ftp://data.pdbj.org/pub/pdb/validation_reports/m7/1m7s | 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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-Components
#1: Protein | Mass: 54042.305 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas syringae (bacteria) / Gene: CATF / Plasmid: pEC3E56 / Production host: Escherichia coli (E. coli) / Strain (production host): UM255 / References: UniProt: P46206, catalase #2: Chemical | ChemComp-HEM / #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: 2.3 Å3/Da / Density % sol: 46.44 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 4000, sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6 | ||||||||||||||||||||||||
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: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 21, 1999 |
Radiation | Monochromator: DIAMOND CRYSTALS [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 175279 / Num. obs: 175279 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.6 Å2 / Rsym value: 0.084 |
Reflection shell | Resolution: 1.8→1.87 Å / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5.9 / Num. unique all: 17810 / Rsym value: 0.21 / % possible all: 95.1 |
Reflection | *PLUS Lowest resolution: 21.9 Å / Rmerge(I) obs: 0.084 |
Reflection shell | *PLUS % possible obs: 95.1 % / Num. unique obs: 17810 / Rmerge(I) obs: 0.21 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→21.9 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→21.9 Å
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.241 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.294 / Num. reflection Rfree: 900 / Rfactor Rwork: 0.234 / Num. reflection Rwork: 16910 |