+Open data
-Basic information
Entry | Database: PDB / ID: 2ciy | ||||||||||||
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Title | Chloroperoxidase complexed with cyanide and DMSO | ||||||||||||
Components | CHLOROPEROXIDASEChloride peroxidase | ||||||||||||
Keywords | OXIDOREDUCTASE / HEME / IRON / CHLORIDE / MANGANESE / PEROXIDASE / PYRROLIDONE CARBOXYLIC ACID / GLYCOPROTEIN / METAL-BINDING | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | CALDARIOMYCES FUMAGO (fungus) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||||||||
Authors | Kuhnel, K. / Blankenfeldt, W. / Terner, J. / Schlichting, I. | ||||||||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Crystal Structures of Chloroperoxidase with its Bound Substrates and Complexed with Formate, Acetate, and Nitrate. Authors: Kuhnel, K. / Blankenfeldt, W. / Terner, J. / Schlichting, I. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ciy.cif.gz | 92.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ciy.ent.gz | 68.1 KB | Display | PDB format |
PDBx/mmJSON format | 2ciy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/2ciy ftp://data.pdbj.org/pub/pdb/validation_reports/ci/2ciy | HTTPS FTP |
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-Related structure data
Related structure data | 2civC 2ciwC 2cixC 2cizC 2cj0C 2cj1C 2cj2C 1cpoS 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: 32746.885 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-319 / Source method: isolated from a natural source / Details: LEPTOXYPHIUM FUMAGO / Source: (natural) CALDARIOMYCES FUMAGO (fungus) / References: UniProt: P04963, chloride peroxidase |
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-Sugars , 4 types, 15 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose / 2alpha-alpha-mannobiose | #6: Sugar | ChemComp-NAG / | #7: Sugar | ChemComp-MAN / |
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-Non-polymers , 7 types, 405 molecules
#4: Chemical | ChemComp-MN / | ||||||||
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#5: Chemical | ChemComp-HEM / | ||||||||
#8: Chemical | #9: Chemical | ChemComp-EDO / | #10: Chemical | ChemComp-CYN / | #11: Chemical | ChemComp-DMS / | #12: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52 % |
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Crystal grow | pH: 6 Details: CRYSTALLISATION CONDITIONS: 22 % PEG 3000, 0.1 M KBR, 0.1 M CITRATE PH 3.6 CRYSTALS WERE SOAKED IN 50 MM KCN, 200 MM CYCLOPENTANEDIONE, 10 % DMSO, 22 % PEG3000, 0.1 M SODIUM CITRATE PH 6 FOR ...Details: CRYSTALLISATION CONDITIONS: 22 % PEG 3000, 0.1 M KBR, 0.1 M CITRATE PH 3.6 CRYSTALS WERE SOAKED IN 50 MM KCN, 200 MM CYCLOPENTANEDIONE, 10 % DMSO, 22 % PEG3000, 0.1 M SODIUM CITRATE PH 6 FOR 10 MIN AT ROOM TMEPERATURE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.008 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.008 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. obs: 46800 / % possible obs: 92.5 % / Observed criterion σ(I): 3 / Redundancy: 3.4 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.7→1.74 Å / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.2 / % possible all: 64.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CPO Resolution: 1.7→19.84 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.704 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.43 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→19.84 Å
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