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Yorodumi- PDB-8qx0: Ligninolytic manganese peroxidase Ape-MnP1 from Agaricales mushro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qx0 | ||||||
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Title | Ligninolytic manganese peroxidase Ape-MnP1 from Agaricales mushrooms in complex with a manganese ion | ||||||
Components | Peroxidase | ||||||
Keywords | OXIDOREDUCTASE / Manganese peroxidase / Fungal / ligninolytic | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / cellular response to oxidative stress / heme binding / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Agrocybe pediades (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.247 Å | ||||||
Authors | Santillana, E. / Romero, A. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Biotechnol Biofuels Bioprod / Year: 2024 Title: Structure-function characterization of two enzymes from novel subfamilies of manganese peroxidases secreted by the lignocellulose-degrading Agaricales fungi Agrocybe pediades and Cyathus striatus. Authors: Sanchez-Ruiz, M.I. / Santillana, E. / Linde, D. / Romero, A. / Martinez, A.T. / Ruiz-Duenas, F.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qx0.cif.gz | 85.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qx0.ent.gz | 59.3 KB | Display | PDB format |
PDBx/mmJSON format | 8qx0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qx0_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 8qx0_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 8qx0_validation.xml.gz | 16 KB | Display | |
Data in CIF | 8qx0_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/8qx0 ftp://data.pdbj.org/pub/pdb/validation_reports/qx/8qx0 | HTTPS FTP |
-Related structure data
Related structure data | 8qwtC 8qwxC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 34925.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrocybe pediades (fungus) / Gene: D9613_004605 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8H4QK56, manganese peroxidase |
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-Non-polymers , 6 types, 187 molecules
#2: Chemical | ChemComp-MN / | ||||||
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#3: Chemical | ChemComp-HEM / | ||||||
#4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.23 Å3/Da / Density % sol: 44.87 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: 30% P2000 MME, 0,1 M sodium citrate, pH 4.2 |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 1.24→62.29 Å / Num. obs: 81601 / % possible obs: 95.2 % / Redundancy: 3.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.048 / Rrim(I) all: 0.068 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.24→1.27 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3964 / CC1/2: 0.539 / Rpim(I) all: 0.493 / Rrim(I) all: 0.7 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.247→62.284 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 0.784 / SU ML: 0.033 / Cross valid method: FREE R-VALUE / ESU R: 0.046 / ESU R Free: 0.048 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.623 Å2
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Refinement step | Cycle: LAST / Resolution: 1.247→62.284 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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