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Open data
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Basic information
Entry | Database: PDB / ID: 2cag | ||||||
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Title | CATALASE COMPOUND II | ||||||
![]() | CATALASE COMPOUND II | ||||||
![]() | OXIDOREDUCTASE (H2O2 ACCEPTOR) / PEROXIDASE / IRON / HEME / 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 | ![]() ![]() ![]() | ||||||
![]() | Gouet, P. / Jouve, H.M. / Hajdu, J. | ||||||
![]() | ![]() 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. #1: ![]() Title: Crystal Structure of Proteus Mirabilis Pr Catalase with and without Bound Nadph Authors: Gouet, P. / Jouve, H.M. / Dideberg, O. #2: ![]() 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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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108 KB | Display | ![]() |
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PDB format | ![]() | 85.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 805 KB | Display | ![]() |
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Full document | ![]() | 820.7 KB | Display | |
Data in XML | ![]() | 21.3 KB | Display | |
Data in CIF | ![]() | 28.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2cae 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: 55726.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: COMPOUND II WAS OBTAINED BY REDUCING A CRYSTAL CONTAINING THE PROTEIN IN THE COMPOUND I STATE WITH DITHIOTHREITOL Source: (natural) ![]() |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
Compound details | OXYGEN OF THE PROXIMAL TYROSINE 337 IS DEPROTONAT |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.05 Å3/Da / Density % sol: 63 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4-5 ℃ / pH: 7.5 / Method: vapor diffusionDetails: drop solution was mixed with an equal volume of reservoir solution | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: FILM / Date: 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. obs: 19251 / % possible obs: 73 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.076 |
Reflection shell | Resolution: 2.7→2.8 Å / Rmerge(I) obs: 0.42 / % possible all: 75 |
Reflection | *PLUS Num. measured all: 39971 |
Reflection shell | *PLUS % possible obs: 75 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2CAE ![]() 2cae Resolution: 2.7→15 Å / Cross valid method: FREE R / σ(F): 2 Details: COORDINATES FOR RESIDUES 1 - 3 AND 479 - 484 ARE NOT INCLUDED. COORDINATES FOR SIDE CHAINS OF RESIDUES 204, 395, 451 AND 72, 450, 473 ARE NOT OBSERVED BEYOND CARBON CB AND CG RESPECTIVELY ...Details: COORDINATES FOR RESIDUES 1 - 3 AND 479 - 484 ARE NOT INCLUDED. COORDINATES FOR SIDE CHAINS OF RESIDUES 204, 395, 451 AND 72, 450, 473 ARE NOT OBSERVED BEYOND CARBON CB AND CG RESPECTIVELY AND MODELED WITH AN OCCUPANCY OF 0.00 AND A BFACTOR OF 99.99.
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Displacement parameters | Biso mean: 29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→15 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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