+Open data
-Basic information
Entry | Database: PDB / ID: 2isa | ||||||
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Title | Crystal Structure of Vibrio salmonicida catalase | ||||||
Components | Catalase | ||||||
Keywords | OXIDOREDUCTASE / Peroxidase / Heme / Iron / Hydrogen peroxide | ||||||
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 | Vibrio salmonicida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | ||||||
Authors | Riise, E.K. / Lorentzen, M.S. / Helland, R. / Smalas, A.O. / Leiros, H.K.S. / Willassen, N.P. | ||||||
Citation | Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2007 Title: The first structure of a cold-active catalase from Vibrio salmonicida at 1.96A reveals structural aspects of cold adaptation Authors: Riise, E.K. / Lorentzen, M.S. / Helland, R. / Smalas, A.O. / Leiros, H.K.S. / Willassen, N.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2isa.cif.gz | 871.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2isa.ent.gz | 709.6 KB | Display | PDB format |
PDBx/mmJSON format | 2isa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2isa_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
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Full document | 2isa_full_validation.pdf.gz | 3.1 MB | Display | |
Data in XML | 2isa_validation.xml.gz | 184.3 KB | Display | |
Data in CIF | 2isa_validation.cif.gz | 272.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/2isa ftp://data.pdbj.org/pub/pdb/validation_reports/is/2isa | HTTPS FTP |
-Related structure data
Related structure data | 1m85S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 54844.891 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio salmonicida (bacteria) / Species: Aliivibrio salmonicida / Strain: LFI1238 / Plasmid: pET-DEST42 / Production host: Escherichia coli (E. coli) / Strain (production host): UM2 / References: UniProt: Q3LSM1, catalase #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-CL / #5: 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: 2.26 Å3/Da / Density % sol: 45.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2.0M Ammonium sulphate, 2% PEG400, 100mM Na-Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.874 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 7, 2005 / Details: mirrors |
Radiation | Monochromator: channel-cut monochromator Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.874 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→20.089 Å / Num. all: 700270 / Num. obs: 267579 / Redundancy: 2.6 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / Net I/σ(I): 6 |
Reflection shell | Resolution: 1.96→2.06 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 2 / Num. unique all: 267579 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1m85 mutated to fit the Vibrio salmonicida catalase sequence Resolution: 1.97→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.557 / SU ML: 0.102 / Isotropic thermal model: overall temperature factors / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.153 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.011 Å2
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Refinement step | Cycle: LAST / Resolution: 1.97→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.965→2.016 Å / Total num. of bins used: 20
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