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Yorodumi- PDB-8qwt: Ligninolytic manganese peroxidase Cst-MnP1 from Agaricales mushro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qwt | ||||||
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Title | Ligninolytic manganese peroxidase Cst-MnP1 from Agaricales mushrooms in complex with a manganese ion | ||||||
Components | Peroxidase | ||||||
Keywords | OXIDOREDUCTASE / Manganese peroxidase / Fungal / ligninolytic | ||||||
Function / homology | PROTOPORPHYRIN IX CONTAINING FE / : Function and homology information | ||||||
Biological species | Cyathus striatus (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 | 8qwt.cif.gz | 85.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qwt.ent.gz | 60.2 KB | Display | PDB format |
PDBx/mmJSON format | 8qwt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qwt_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8qwt_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8qwt_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 8qwt_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qw/8qwt ftp://data.pdbj.org/pub/pdb/validation_reports/qw/8qwt | HTTPS FTP |
-Related structure data
Related structure data | 8qwxC 8qx0C 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: 34412.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cyathus striatus (fungus) / Production host: Escherichia coli (E. coli) / References: manganese peroxidase |
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-Non-polymers , 7 types, 182 molecules
#2: Chemical | ChemComp-HEM / | ||||||||
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#3: Chemical | ChemComp-MN / | ||||||||
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-PG4 / #7: Chemical | ChemComp-GOL / | #8: 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: 2.16 Å3/Da / Density % sol: 43.08 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG 8000, 0,1 M Tris-HCl, pH 7, 0,3M MgCl2 |
-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: Jul 25, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→56.64 Å / Num. obs: 48414 / % possible obs: 99.9 % / Redundancy: 5.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.076 / Rrim(I) all: 0.138 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 1.5→1.53 Å / Rmerge(I) obs: 1.147 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2237 / CC1/2: 0.638 / Rpim(I) all: 0.773 / Rrim(I) all: 1.389 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→54.755 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.186 / WRfactor Rwork: 0.159 / SU B: 1.666 / SU ML: 0.058 / Average fsc free: 0.9627 / Average fsc work: 0.9693 / Cross valid method: FREE R-VALUE / ESU R: 0.069 / ESU R Free: 0.07 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: 16.86 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→54.755 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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