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Yorodumi- PDB-1e93: High resolution structure and biochemical properties of a recombi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1.0E+93 | ||||||
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Title | High resolution structure and biochemical properties of a recombinant catalase depleted in iron | ||||||
Components | CATALASE | ||||||
Keywords | OXIDOREDUCTASE / OXIDOREDUCTASE (H2O2 ACCEPTOR) / PEROXIDASE / IRON / HEM / HYDROGEN PEROXIDE / NADP | ||||||
Function / homology | Function and homology information catalase / catalase activity / hydrogen peroxide catabolic process / response to hydrogen peroxide / heme binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | PROTEUS MIRABILIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Andreoletti, P. / Sainz, G. / Jaquinod, M. / Gagnon, J. / Jouve, H.M. | ||||||
Citation | Journal: Proteins: Struct.,Funct., Genet. / Year: 2003 Title: High-Resolution Structure and Biochemical Properties of a Recombinant Proteus Mirabilis Catalase Depleted in Iron. Authors: Andreoletti, P. / Sainz, G. / Jaquinod, M. / Gagnon, J. / Jouve, H.M. #1: Journal: J.Mol.Biol. / Year: 1995 Title: Crystal Structure of Proteus Mirabilis Pr Catalase with and without Bound Nadph Authors: Gouet, P. / Jouve, H.M. / Dideberg, O. #2: Journal: J.Mol.Biol. / Year: 1991 Title: Crystallization and Crystal Packing of Proteus Mirabilis Pr Catalase Authors: Jouve, H.M. / Gouet, P. / Boudjada, N. / Buisson, G. / Kahn, R. / Duee, E. #3: Journal: Acta Crystallogr.,Sect.B / Year: 1986 Title: The Refined Structure of Beef Liver Catalase at 2.5 Angstroms Resolution Authors: Fita, I. / Silva, A.M. / Murthy, M.R.N. / Rossmann, M.G. #4: Journal: Nat.Struct.Biol. / Year: 1996 Title: Ferryl Intermediates of Catalase Captured by Time-Resolved Weissenberg Crystallography and Uv-Vis Spectroscopy Authors: Gouet, P. / Jouve, H.M. / Williams, P.A. / Andersson, I. / Andreoletti, P. / Nussaume, L. / Hajdu, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e93.cif.gz | 126.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e93.ent.gz | 95.7 KB | Display | PDB format |
PDBx/mmJSON format | 1e93.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e93_validation.pdf.gz | 820.9 KB | Display | wwPDB validaton report |
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Full document | 1e93_full_validation.pdf.gz | 824.4 KB | Display | |
Data in XML | 1e93_validation.xml.gz | 26 KB | Display | |
Data in CIF | 1e93_validation.cif.gz | 39.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/1e93 ftp://data.pdbj.org/pub/pdb/validation_reports/e9/1e93 | HTTPS FTP |
-Related structure data
Related structure data | 1h6nC 1cae 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 55726.414 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: METHIONINE SULFONE IN POSITION 53 TYROSINE 337 LACK THE HYDROXYL HYDROGEN Source: (gene. exp.) PROTEUS MIRABILIS (bacteria) / Gene: KATA / Plasmid: PALTER-CAT / Gene (production host): KATA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 DE3 / References: UniProt: P42321, catalase |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-ACT / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
Compound details | CONVERSION OF HYDROGEN PEROXIDE IN WATER AND OXYGEN PROTECTS CELLS FROM THE TOXIC EFFECTS OF ...CONVERSION |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.82 Å3/Da / Density % sol: 63 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: HANGING DROP AT 4 DEGREE C, pH 7.30 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4-5 ℃ / pH: 7.5 / Method: vapor diffusion, hanging dropDetails: drop was mixed with an equal volume of reservoir solution | ||||||||||||||||||||||||||||||||||||||||||
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: BM14 / Wavelength: 0.9574 |
Detector | Detector: IMAGE PLATE / Date: Jul 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9574 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 58298 / % possible obs: 97.7 % / Observed criterion σ(I): 3 / Redundancy: 4.46 % / Biso Wilson estimate: 12.9 Å2 / Rsym value: 0.072 |
Reflection shell | Resolution: 2→2.05 Å / Rsym value: 0.22 / % possible all: 94.6 |
Reflection | *PLUS % possible obs: 97.8 % / Redundancy: 5.7 % / Num. measured all: 332299 / Rmerge(I) obs: 0.072 |
Reflection shell | *PLUS % possible obs: 94.6 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.22 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CAE 1cae Resolution: 2→14.95 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3292293.35 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: AMINO ACIDS 358 - 362 ARE POORLY VISIBLE IN THE ELECTRON DENSITY MAP THE 5 C-TERMINAL RESIDUES WAS NOT SEEN IN THE DENSITY MAPS
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 29.6112 Å2 / ksol: 0.333625 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→14.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.12 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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