+Open data
-Basic information
Entry | Database: PDB / ID: 3m5q | |||||||||
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Title | 0.93 A Structure of Manganese-Bound Manganese Peroxidase | |||||||||
Components | Manganese peroxidase 1 | |||||||||
Keywords | OXIDOREDUCTASE / Peroxidase / Heme / Mn(II)-binding site / Ca(II)-binding site / Glycosylation / Ultrahigh resolution / Calcium / Disulfide bond / Glycoprotein / Hydrogen peroxide / Iron / Lignin degradation / Manganese / Metal-binding / Secreted | |||||||||
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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 0.93 Å | |||||||||
Authors | Sundaramoorthy, M. / Gold, M.H. / Poulos, T.L. | |||||||||
Citation | Journal: J.Inorg.Biochem. / Year: 2010 Title: Ultrahigh (0.93A) resolution structure of manganese peroxidase from Phanerochaete chrysosporium: implications for the catalytic mechanism. Authors: Sundaramoorthy, M. / Gold, M.H. / Poulos, T.L. #1: 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. #2: 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.H. / 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 | 3m5q.cif.gz | 171.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m5q.ent.gz | 133.3 KB | Display | PDB format |
PDBx/mmJSON format | 3m5q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3m5q_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 3m5q_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 3m5q_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 3m5q_validation.cif.gz | 32.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/3m5q ftp://data.pdbj.org/pub/pdb/validation_reports/m5/3m5q | HTTPS FTP |
-Related structure data
Related structure data | 3m8mC 1yydS 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 / 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 , 5 types, 481 molecules
#4: Chemical | #5: Chemical | ChemComp-MN / | #6: Chemical | ChemComp-GOL / | #7: Chemical | ChemComp-HEM / | #8: 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: 2.54 Å3/Da / Density % sol: 51.62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% PEG 8000, 0.2 M ammonium sulfate, 0.1 M sodium cacodylate, pH 6.5, Vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 1, 1999 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 0.93→160 Å / Num. obs: 264958 / % possible obs: 93 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rsym value: 0.066 / Net I/σ(I): 26.3 |
Reflection shell | Resolution: 0.93→0.95 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.512 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1YYD Resolution: 0.93→8 Å / Num. parameters: 29226 / Num. restraintsaints: 35571 / Occupancy max: 1.02 / Occupancy min: 0.52 / Cross valid method: FREE R / σ(F): 2 / σ(I): 4 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 3.6%
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 126.62 Å2 / Biso mean: 13.927 Å2 / Biso min: 5.42 Å2 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.93→8 Å
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Refine LS restraints |
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