+Open data
-Basic information
Entry | Database: PDB / ID: 1qf7 | ||||||
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Title | STRUCTURE OF THE MUTANT HIS392GLN OF CATALASE HPII FROM E. COLI | ||||||
Components | PROTEIN (CATALASE HPII) | ||||||
Keywords | OXIDOREDUCTASE / COVALENT MODIFICATIONS | ||||||
Function / homology | Function and homology information catalase / hyperosmotic response / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / iron ion binding / DNA damage response / heme binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 2.2 Å | ||||||
Authors | Mate, M.J. / Loewen, P.C. / Fita, I. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1999 Title: Mutants that alter the covalent structure of catalase hydroperoxidase II from Escherichia coli. Authors: Mate, M.J. / Sevinc, M.S. / Hu, B. / Bujons, J. / Bravo, J. / Switala, J. / Ens, W. / Loewen, P.C. / Fita, I. #1: Journal: Proteins / Year: 1999 Title: Structure of catalase HPII from Escherichia coli at 1.9 A resolution. Authors: Bravo, J. / Mate, M.J. / Schneider, T. / Switala, J. / Wilson, K. / Loewen, P.C. / Fita, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qf7.cif.gz | 631.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qf7.ent.gz | 510.4 KB | Display | PDB format |
PDBx/mmJSON format | 1qf7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qf/1qf7 ftp://data.pdbj.org/pub/pdb/validation_reports/qf/1qf7 | HTTPS FTP |
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-Related structure data
Related structure data | 1cf9C 1iphS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 84261.438 Da / Num. of mol.: 4 / Mutation: H392Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PAMKATE72 / Gene (production host): KATE / Production host: Escherichia coli (E. coli) / References: UniProt: P21179, 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: 2.11 Å3/Da / Density % sol: 41.74 % | ||||||||||||||||||||||||
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Crystal grow | pH: 9 / Details: pH 9 | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 9 / Method: vapor diffusion, hanging drop / Details: Bravo, J., (1995) Structure, 3, 491. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Detector: IMAGE PLATE / Date: Oct 1, 1998 |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→20 Å / Num. obs: 137604 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 13.63 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.09 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.12→2.2 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5.1 / Rsym value: 0.25 / % possible all: 95 |
Reflection shell | *PLUS % possible obs: 95 % |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: PDB ENTRY 1IPH Resolution: 2.2→20 Å / SU B: 5.565 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.318 / ESU R Free: 0.211
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Displacement parameters | Biso mean: 13.55 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.144 / Rfactor Rfree: 0.21 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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