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Yorodumi- PDB-3kuo: X-ray structure of the metcyano form of dehaloperoxidase from amp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kuo | ||||||
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Title | X-ray structure of the metcyano form of dehaloperoxidase from amphitrite ornata: evidence for photoreductive lysis of iron-cyanide bond | ||||||
Components | Dehaloperoxidase A | ||||||
Keywords | OXIDOREDUCTASE / Crystal structure of metcyano form of dehaloperoxydase / heme / oxygen transport / peroxidase / transport / transport protein | ||||||
Function / homology | Function and homology information oxygen carrier activity / oxygen binding / peroxidase activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Amphitrite ornata (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å | ||||||
Authors | Serrano, V.S. / Chen, Z. / Gaff, J.F. / Rose, R. / Franzen, S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2010 Title: X-ray structure of the metcyano form of dehaloperoxidase from Amphitrite ornata: evidence for photoreductive dissociation of the iron-cyanide bond. Authors: de Serrano, V.S. / Davis, M.F. / Gaff, J.F. / Zhang, Q. / Chen, Z. / D'Antonio, E.L. / Bowden, E.F. / Rose, R. / Franzen, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kuo.cif.gz | 167.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kuo.ent.gz | 136.3 KB | Display | PDB format |
PDBx/mmJSON format | 3kuo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kuo_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 3kuo_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 3kuo_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 3kuo_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/3kuo ftp://data.pdbj.org/pub/pdb/validation_reports/ku/3kuo | HTTPS FTP |
-Related structure data
Related structure data | 3kunC 1ew6S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15532.532 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Amphitrite ornata (invertebrata) / Gene: DHPA / Plasmid: pET16B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9NAV8 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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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: 2.11 Å3/Da / Density % sol: 41.62 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: 0.2 M AMMONIUM SULFATE, 34% PEG 4000, PH 5.9, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 / Wavelength: 1 Å | |||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 3, 2007 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.26→35 Å / Num. obs: 66582 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 14.63 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 25.36 | |||||||||
Reflection shell | Resolution: 1.26→1.29 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 2 / Num. unique all: 4897 / % possible all: 93.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EW6 Resolution: 1.26→35 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.988 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.069 / ESU R Free: 0.058 / 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: 14.63 Å2
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Refinement step | Cycle: LAST / Resolution: 1.26→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.26→1.29 Å / Total num. of bins used: 20
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