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Yorodumi- PDB-7znm: Artificial Unspecific Peroxygenase expressed in Pichia pastoris a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7znm | ||||||
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Title | Artificial Unspecific Peroxygenase expressed in Pichia pastoris at 2.01 Angstrom resolution | ||||||
Components | Artificial Unspecific Peroxygenase | ||||||
Keywords | OXIDOREDUCTASE / Heme / peroxygenase / UPO | ||||||
Function / homology | PROTOPORPHYRIN IX CONTAINING FE Function and homology information | ||||||
Biological species | Marasmius rotula (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | ||||||
Authors | Robinson, W.X.Q. / Mielke, T. / Grogan, G. | ||||||
Funding support | 1items
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Citation | Journal: Chembiochem / Year: 2023 Title: Comparing the Catalytic and Structural Characteristics of a 'Short' Unspecific Peroxygenase (UPO) Expressed in Pichia pastoris and Escherichia coli. Authors: Robinson, W.X.Q. / Mielke, T. / Melling, B. / Cuetos, A. / Parkin, A. / Unsworth, W.P. / Cartwright, J. / Grogan, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7znm.cif.gz | 117.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7znm.ent.gz | 89 KB | Display | PDB format |
PDBx/mmJSON format | 7znm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zn/7znm ftp://data.pdbj.org/pub/pdb/validation_reports/zn/7znm | HTTPS FTP |
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-Related structure data
Related structure data | 7znvC 7znwC 5fujS S: Starting model for refinement 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 0 / Auth seq-ID: 9 - 238 / Label seq-ID: 9 - 238
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 26476.498 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Marasmius rotula (fungus) / Production host: Komagataella pastoris (fungus) / References: unspecific peroxygenase |
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-Sugars , 2 types, 6 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 351 molecules
#3: Chemical | #5: Chemical | #6: Chemical | ChemComp-CL / #7: Water | ChemComp-HOH / | |
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-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: 2.73 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.1 / Details: 0.2 M CaCl2 20% (w/v) PEG 3350 pH 5.1 |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976254 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 8, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976254 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→50.57 Å / Num. obs: 39554 / % possible obs: 99.9 % / Redundancy: 8 % / Biso Wilson estimate: 20 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.04 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.01→2.06 Å / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 2861 / CC1/2: 0.96 / Rpim(I) all: 0.28 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5FUJ Resolution: 2.01→47.82 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.214 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.54 Å2 / Biso mean: 28.33 Å2 / Biso min: 16.9 Å2
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Refinement step | Cycle: final / Resolution: 2.01→47.82 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 7710 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.01→2.062 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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