+Open data
-Basic information
Entry | Database: PDB / ID: 1a4e | ||||||
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Title | CATALASE A FROM SACCHAROMYCES CEREVISIAE | ||||||
Components | CATALASE A | ||||||
Keywords | OXIDOREDUCTASE / CATALASE / PEROXIDASE | ||||||
Function / homology | Function and homology information : / catalase / catalase activity / peroxisomal matrix / response to reactive oxygen species / hydrogen peroxide catabolic process / response to hydrogen peroxide / peroxisome / mitochondrial matrix / heme binding ...: / catalase / catalase activity / peroxisomal matrix / response to reactive oxygen species / hydrogen peroxide catabolic process / response to hydrogen peroxide / peroxisome / mitochondrial matrix / heme binding / mitochondrion / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Mate, M.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Structure of catalase-A from Saccharomyces cerevisiae. Authors: Mate, M.J. / Zamocky, M. / Nykyri, L.M. / Herzog, C. / Alzari, P.M. / Betzel, C. / Koller, F. / Fita, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a4e.cif.gz | 415.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a4e.ent.gz | 337.7 KB | Display | PDB format |
PDBx/mmJSON format | 1a4e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a4e_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 1a4e_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 1a4e_validation.xml.gz | 80.6 KB | Display | |
Data in CIF | 1a4e_validation.cif.gz | 112.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/1a4e ftp://data.pdbj.org/pub/pdb/validation_reports/a4/1a4e | HTTPS FTP |
-Related structure data
Related structure data | 7catS 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 55623.930 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cellular location: PEROXISOMES / References: UniProt: P15202, catalase #2: Chemical | ChemComp-AZI / #3: Chemical | #4: Chemical | ChemComp-HEM / #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: 3.35 Å3/Da / Density % sol: 60 % | ||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: pH 8.5 | ||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Type: EMBL/DESY, HAMBURG / Wavelength: 0.928 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.928 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→30 Å / Num. obs: 123230 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 33.6 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 25.12 |
Reflection shell | Resolution: 2.35→2.39 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 5.69 / Rsym value: 0.33 / % possible all: 94.5 |
Reflection | *PLUS Num. measured all: 1276062 |
Reflection shell | *PLUS % possible obs: 95 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 7CAT Resolution: 2.4→20 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 33.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.49 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 10
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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