+Open data
-Basic information
Entry | Database: PDB / ID: 1yzp | |||||||||
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Title | Substrate-free manganese peroxidase | |||||||||
Components | Peroxidase manganese-dependent I | |||||||||
Keywords | OXIDOREDUCTASE / Peroxidase / heme enzyme / Mn-binding protein / Ca-binding site / glycosylation | |||||||||
Function / homology | Function and homology information manganese peroxidase / manganese peroxidase activity / lignin catabolic process / 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 | Phanerochaete chrysosporium (fungus) | |||||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.6 Å | |||||||||
Authors | Sundaramoorthy, M. / Youngs, H.L. / Gold, M.H. / Poulos, T.L. | |||||||||
Citation | Journal: Biochemistry / Year: 2005 Title: High-Resolution Crystal Structure of Manganese Peroxidase: Substrate and Inhibitor Complexes. Authors: Sundaramoorthy, M. / Youngs, H.L. / Gold, M.H. / Poulos, T.L. #1: Journal: J.Biol.Chem. / Year: 1994 Title: The crystal structure of manganese peroxidase from Phanerochaete chrysosporium at 2.06 A resolution Authors: Sundaramoorthy, M. / Kishi, K. / Gold, M.G. / Poulos, T.L. #2: Journal: J.Biol.Chem. / Year: 1997 Title: Crystal structures of substrate binding site mutants of manganese peroxidase Authors: Sundaramoorthy, M. / Kishi, K. / Gold, M.G. / Poulos, T.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yzp.cif.gz | 97.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yzp.ent.gz | 71.4 KB | Display | PDB format |
PDBx/mmJSON format | 1yzp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yzp_validation.pdf.gz | 559.4 KB | Display | wwPDB validaton report |
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Full document | 1yzp_full_validation.pdf.gz | 561.2 KB | Display | |
Data in XML | 1yzp_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 1yzp_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/1yzp ftp://data.pdbj.org/pub/pdb/validation_reports/yz/1yzp | HTTPS FTP |
-Related structure data
Related structure data | 1yydSC 1yygC 1yzrC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37482.973 Da / Num. of mol.: 1 / Fragment: Manganese peroxidase / Source method: isolated from a natural source / Source: (natural) Phanerochaete chrysosporium (fungus) / References: UniProt: Q02567, manganese peroxidase |
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-Sugars , 2 types, 2 molecules
#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 |
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#3: Sugar | ChemComp-MAN / |
-Non-polymers , 4 types, 547 molecules
#4: Chemical | #5: Chemical | ChemComp-HEM / | #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8K, sodium cacodylate, ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 19, 1998 / Details: Mirrors |
Radiation | Monochromator: Yale mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→161 Å / Num. all: 44812 / Num. obs: 43385 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.043 |
Reflection shell | Resolution: 1.6→1.68 Å / % possible all: 55 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: pdb entry 1YYD Resolution: 1.6→8 Å / Cross valid method: throught / σ(F): 4 / Stereochemistry target values: SHELXL
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Refinement step | Cycle: LAST / Resolution: 1.6→8 Å
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Refine LS restraints |
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