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- PDB-1h7k: Formation of a tyrosyl radical intermediate in Proteus mirabilis ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1h7k | ||||||
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Title | Formation of a tyrosyl radical intermediate in Proteus mirabilis catalase by directed mutagenesis and consequences for nucleotide reactivity | ||||||
![]() | CATALASE | ||||||
![]() | OXIDOREDUCTASE / OXIDOREDUCTASE (H2O2 ACCEPTOR) / PEROXIDASE / IRON / HEM / HYDROGEN PEROXIDE / NADP | ||||||
Function / homology | ![]() catalase / catalase activity / hydrogen peroxide catabolic process / response to hydrogen peroxide / heme binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Andreoletti, P. / Gambarelli, S. / Gaillard, J. / Sainz, G. / Stojanoff, V. / Jouve, H.M. | ||||||
![]() | ![]() Title: Formation of a Tyrosyl Radical Intermediate in Proteus Mirabilis Catalase by Directed Mutagenesis and Consequences for Nucleotide Reactivity. Authors: Andreoletti, P. / Gambarelli, S. / Sainz, G. / Stojanoff, V. / White, C. / Desfonds, G. / Gagnon, J. / Gaillard, J. / Jouve, H.M. #1: ![]() 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. #2: ![]() Title: Crystal Structure of Proteus Mirabilis Pr Catalase with and without Bound Nadph Authors: Gouet, P. / Jouve, H.M. / Dideberg, O. #3: 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. #4: ![]() 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. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 117.2 KB | Display | ![]() |
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PDB format | ![]() | 88 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 830.8 KB | Display | ![]() |
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Full document | ![]() | 838.3 KB | Display | |
Data in XML | ![]() | 22.1 KB | Display | |
Data in CIF | ![]() | 30.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1cae S: Starting model for refinement |
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Similar structure data |
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Links
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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: 55611.152 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.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-ACT / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
Sequence details | MODRES: 1H7K OMT A 53() METHIONINE SULFONE (S-DIOXYMETHIONINE) MODRES: 1H7K TYR A 337() OXYGEN OF ...MODRES: 1H7K OMT A 53() METHIONINE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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 DEG C, pH 7.30 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4-5 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Jouve, H.M., (1991) J.Mol.Biol., 221, 1075. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / 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: 2.4→29.26 Å / Num. obs: 35932 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 15.8 % / Biso Wilson estimate: 40 Å2 |
Reflection shell | Resolution: 2→2.05 Å / % possible all: 94.6 |
Reflection | *PLUS Redundancy: 15.8 % / Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS % possible obs: 99.9 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.251 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1CAE ![]() 1cae Resolution: 2.4→29.26 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2727867.74 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: AMINO ACIDS 358 - 362 ARE NOT REFINED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.7587 Å2 / ksol: 0.306189 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→29.26 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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Refinement | *PLUS Lowest resolution: 15 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.24 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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