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Yorodumi- PDB-3dr9: Increased Distal Histidine Conformational Flexibility in the Deox... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dr9 | ||||||
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Title | Increased Distal Histidine Conformational Flexibility in the Deoxy Form of Dehaloperoxidase from Amphitrite ornata | ||||||
Components | Dehaloperoxidase A | ||||||
Keywords | OXIDOREDUCTASE / deoxy form of dehaloperoxidase / DHP / heme peroxidase / globin-like / globin / heme protein / Heme / Oxygen transport / Peroxidase / Transport | ||||||
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 / molecular replacement / Resolution: 1.26 Å | ||||||
Authors | Chen, X. / de Serrano, V.S. / Betts, L. / Franzen, S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2009 Title: Distal histidine conformational flexibility in dehaloperoxidase from Amphitrite ornata. Authors: Chen, Z. / de Serrano, V. / Betts, L. / Franzen, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dr9.cif.gz | 156.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dr9.ent.gz | 125.7 KB | Display | PDB format |
PDBx/mmJSON format | 3dr9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dr9_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 3dr9_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 3dr9_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 3dr9_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/3dr9 ftp://data.pdbj.org/pub/pdb/validation_reports/dr/3dr9 | HTTPS FTP |
-Related structure data
Similar structure data |
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-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: 15548.597 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): Rosetta(DE3)pLysS / References: UniProt: Q9NAV8 #2: Chemical | #3: Chemical | #4: 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: 2.15 Å3/Da / Density % sol: 42.7 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: 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 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 22, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.22→35 Å / Num. obs: 79486 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.22→1.26 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.513 / % possible all: 92.5 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.26→5 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 0 / SU B: 1.861 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.055 / 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: 11.637 Å2
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Refinement step | Cycle: LAST / Resolution: 1.26→5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.26→1.291 Å / Total num. of bins used: 20
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