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Open data
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Basic information
Entry | Database: PDB / ID: 1gza | |||||||||
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Title | PEROXIDASE | |||||||||
![]() | PEROXIDASE | |||||||||
![]() | OXIDOREDUCTASE / GLYCOPROTEIN / PEROXIDASE / HEME | |||||||||
Function / homology | ![]() lactoperoxidase activity / peroxidase / response to reactive oxygen species / hydrogen peroxide catabolic process / cellular response to oxidative stress / heme binding / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Fukuyama, K. / Itakura, H. | |||||||||
![]() | ![]() Title: Binding of iodide to Arthromyces ramosus peroxidase investigated with X-ray crystallographic analysis, 1H and 127I NMR spectroscopy, and steady-state kinetics. Authors: Fukuyama, K. / Sato, K. / Itakura, H. / Takahashi, S. / Hosoya, T. #1: ![]() Title: Pentacoordination of the Heme Iron of Arthromyces Ramosus Peroxidase Shown by a 1.8 A Resolution Crystallographic Study at Ph 4.5 Authors: Kunishima, N. / Amada, F. / Fukuyama, K. / Kawamoto, M. / Matsunaga, T. / Matsubara, H. #2: ![]() 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. #3: ![]() Title: Crystal Structure of the Fungal Peroxidase from Arthromyces Ramosus at 1.9 A Resolution. Structural Comparisons with the Lignin and Cytochrome C Peroxidases Authors: Kunishima, N. / Fukuyama, K. / Matsubara, H. / Hatanaka, H. / Shibano, Y. / Amachi, T. #4: ![]() 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 | ![]() | 78.7 KB | Display | ![]() |
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PDB format | ![]() | 60.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 539.6 KB | Display | ![]() |
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Full document | ![]() | 546.2 KB | Display | |
Data in XML | ![]() | 9.4 KB | Display | |
Data in CIF | ![]() | 14.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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Details | THE ASYMMETRIC UNIT OF THE CRYSTAL CONTAINS ONE MOLECULE. |
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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 5.5 / 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, 251 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-IOD / | #5: Chemical | ChemComp-HEM / | #6: Water | ChemComp-HOH / | |
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-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: 5.5 / Details: pH 5.5 | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22-26 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop / Details: repeated seeding | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ![]() |
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Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.06 Å / Num. obs: 20178 / % possible obs: 95.3 % / Num. measured all: 125031 / Rmerge(I) obs: 0.062 |
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Processing
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Refinement | Resolution: 2.06→7 Å / Rfactor Rwork: 0.162 / Rfactor obs: 0.162 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.06→7 Å
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Refine LS restraints |
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Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |