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- PDB-1aru: CRYSTAL STRUCTURES OF CYANIDE-AND TRIIODIDE-BOUND FORMS OF ARTHRO... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1aru | |||||||||
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Title | CRYSTAL STRUCTURES OF CYANIDE-AND TRIIODIDE-BOUND FORMS OF ARTHROMYCES RAMOSUS PEROXIDASE AT DIFFERENT PH VALUES. PERTURBATIONS OF ACTIVE SITE RESIDUES AND THEIR IMPLICATION IN ENZYME CATALYSIS | |||||||||
![]() | PEROXIDASE![]() | |||||||||
![]() | PEROXIDASE (DONOR:H2O2 OXIDOREDUCTASE) | |||||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Fukuyama, K. / Kunishima, N. / Amada, F. | |||||||||
![]() | ![]() Title: Crystal structures of cyanide- and triiodide-bound forms of Arthromyces ramosus peroxidase at different pH values. Perturbations of active site residues and their implication in enzyme catalysis. Authors: Fukuyama, K. / Kunishima, N. / Amada, F. / Kubota, T. / Matsubara, H. #1: ![]() Title: Crystal Structure of the Fungal Peroxidase from Arthromyces Ramosus at 1.9 Angstroms Resolution: Structural Comparisons with the Lignin and Cytochrome C Peroxidases Authors: Kunishima, N. / Fukuyama, K. / Matsubara, H. / Hatanaka, H. / Shibano, Y. / Amachi, T. #2: ![]() Title: Crystallization and Preliminary X-Ray Diffraction Studies of Peroxidase from a Fungus Arthromyces Ramosus Authors: Kunishima, N. / Fukuyama, K. / Wakabayashi, S. / Sumida, M. / Takaya, M. / Shibano, Y. / Amachi, T. / Matsubara, H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.2 KB | Display | ![]() |
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PDB format | ![]() | 61.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | ![]() Mass: 35722.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PH 7.5 / Source: (natural) ![]() ![]() |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose![]() Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 310 molecules ![](data/chem/img/CYN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CYN / ![]() | ||||
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#4: Chemical | #5: Chemical | ChemComp-HEM / | ![]() #6: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.14 % | ||||||||||||||||||||
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Crystal grow![]() | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 24 ℃ / Method: vapor diffusion, hanging drop / Details: seeding | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | *PLUS Highest resolution: 1.6 Å / Num. obs: 37405 / % possible obs: 84.3 % / Num. measured all: 163223 / Rmerge(I) obs: 0.063 |
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Processing
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Refinement | Resolution: 1.6→7 Å / Rfactor Rwork![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→7 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 36860 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 16.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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