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Yorodumi- PDB-7rst: The Crystal Structure of Recombinant Chloroperoxidase Expressed i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rst | ||||||
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Title | The Crystal Structure of Recombinant Chloroperoxidase Expressed in Aspergillus niger | ||||||
Components | ChloroperoxidaseChloride peroxidase | ||||||
Keywords | OXIDOREDUCTASE / recombinant chloroperoxidase / Aspergillus niger | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Leptoxyphium fumago (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å | ||||||
Authors | Tang, X. / Venkadesh, S. / Zhou, J. / Rosen, B. / Wang, X. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: The Crystal Structure of Recombinant Chloroperoxidase Expressed in Aspergillus niger Authors: Tang, X. / Venkadesh, S. / Zhou, J. / Rosen, B. / Wang, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rst.cif.gz | 96 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rst.ent.gz | 69.2 KB | Display | PDB format |
PDBx/mmJSON format | 7rst.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rs/7rst ftp://data.pdbj.org/pub/pdb/validation_reports/rs/7rst | HTTPS FTP |
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-Related structure data
Related structure data | 2cpoS S: Starting model for refinement |
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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: 32746.885 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leptoxyphium fumago (fungus) / Gene: CPO / Production host: Aspergillus niger (mold) / References: UniProt: P04963, chloride peroxidase |
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-Sugars , 4 types, 16 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / | #7: Sugar | ChemComp-MAN / |
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-Non-polymers , 4 types, 480 molecules
#4: Chemical | ChemComp-MN / | ||
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#5: Chemical | ChemComp-HEM / | ||
#8: Chemical | ChemComp-IOD / #9: 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: 3.37 Å3/Da / Density % sol: 63.51 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2M NaI, 20% polyethyleneglycol (PEG) 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9999 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→37.3 Å / Num. obs: 45316 / % possible obs: 90.5 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.69→1.78 Å / Rmerge(I) obs: 0.597 / Num. unique obs: 7220 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CPO Resolution: 1.69→30.36 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.62 / 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 max: 97.76 Å2 / Biso mean: 22.0758 Å2 / Biso min: 8.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.69→30.36 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16
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