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Yorodumi- PDB-4czr: Crystal structure of the extralong fungal manganese peroxidase fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4czr | ||||||
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Title | Crystal structure of the extralong fungal manganese peroxidase from Ceriporiopsis subvermispora in complex with cadmium (anomalous data) | ||||||
Components | EXTRALONG MANGANESE PEROXIDASE | ||||||
Keywords | OXIDOREDUCTASE / CLASS II (FUNGAL) PEROXIDASES / PROTOPORPHYRIN IX / ELECTRON TRANSFER / LIGNIN PEROXIDASE / LIGNIN DEGRADATION / MANGANESE PEROXIDASE / MNII OXIDATION / PEROXIDASE / HYDROGEN PEROXIDE / METAL-BINDING / SECRETED | ||||||
Function / homology | Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Orthogonal Bundle / Mainly Alpha / : / PROTOPORPHYRIN IX CONTAINING FE Function and homology information | ||||||
Biological species | CERIPORIOPSIS SUBVERMISPORA (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.984 Å | ||||||
Authors | Medrano, F.J. / Romero, A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structural Implications of the C-Terminal Tail in the Catalytic and Stability Properties of Manganese Peroxidases from Ligninolytic Fungi Authors: Fernandez-Fueyo, E. / Acebes, S. / Ruiz-Duenas, F.J. / Martinez, M.J. / Romero, A. / Medrano, F.J. / Guallar, V. / Martinez, A.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4czr.cif.gz | 92.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4czr.ent.gz | 68.4 KB | Display | PDB format |
PDBx/mmJSON format | 4czr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/4czr ftp://data.pdbj.org/pub/pdb/validation_reports/cz/4czr | HTTPS FTP |
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-Related structure data
Related structure data | 4cznC 4czoC 4czpC 4czqC 3mq5 C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 38747.152 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CERIPORIOPSIS SUBVERMISPORA (fungus) / Plasmid: PFLAG1-CSMNP6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 SUBSTR. W3110 / References: manganese peroxidase |
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-Non-polymers , 5 types, 341 molecules
#2: Chemical | #3: Chemical | ChemComp-HEM / | #4: Chemical | #5: Chemical | #6: 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: 2.5 Å3/Da / Density % sol: 50.77 % / Description: NONE |
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Crystal grow | pH: 4.6 / Details: 18% PEG 4000, 100MM NA-ACETATE PH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.92224 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.92224 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→40 Å / Num. obs: 47444 / % possible obs: 87.4 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 22.39 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 42.6 |
Reflection shell | Resolution: 1.98→2.1 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 7.3 / % possible all: 33.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3MQ5 3mq5 Resolution: 1.984→48.648 Å / SU ML: 0.18 / σ(F): 1.38 / Phase error: 18.93 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.984→48.648 Å
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Refine LS restraints |
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LS refinement shell |
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