+Open data
-Basic information
Entry | Database: PDB / ID: 1gzb | |||||||||
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Title | PEROXIDASE | |||||||||
Components | PEROXIDASE | |||||||||
Keywords | OXIDOREDUCTASE / GLYCOPROTEIN / PEROXIDASE / HEME | |||||||||
Function / homology | Function and homology information 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 | 'Arthromyces ramosus' (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å | |||||||||
Authors | Fukuyama, K. / Kunishima, N. / Amada, F. | |||||||||
Citation | Journal: FEBS Lett. / Year: 1996 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. #1: Journal: J.Biol.Chem. / Year: 1995 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. #2: Journal: J.Mol.Biol. / Year: 1994 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. #3: Journal: Proteins / Year: 1993 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gzb.cif.gz | 79.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gzb.ent.gz | 61.1 KB | Display | PDB format |
PDBx/mmJSON format | 1gzb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gzb_validation.pdf.gz | 540 KB | Display | wwPDB validaton report |
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Full document | 1gzb_full_validation.pdf.gz | 545.7 KB | Display | |
Data in XML | 1gzb_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 1gzb_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/1gzb ftp://data.pdbj.org/pub/pdb/validation_reports/gz/1gzb | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-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. |
-Components
#1: Protein | Mass: 35722.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PH 4.5 / Source: (natural) 'Arthromyces ramosus' (fungus) / Genus: 'Arthromyces' / References: UniProt: P28313, peroxidase | ||||
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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 | ||||
#3: Chemical | #4: Chemical | ChemComp-HEM / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.14 % | ||||||||||||||||||||
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Crystal grow | pH: 4.5 / Details: pH 4.5 | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22-24 ℃ / 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: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
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Detector | Detector: FILM |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.8 Å / Num. obs: 28453 / % possible obs: 90.4 % / Num. measured all: 171644 / Rmerge(I) obs: 0.0698 |
-Processing
Software |
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Refinement | Resolution: 1.8→7 Å / Rfactor Rwork: 0.188 / Rfactor obs: 0.188 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→7 Å
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Refine LS restraints |
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Refinement | *PLUS Num. reflection obs: 27884 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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