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Yorodumi- PDB-2oif: The crystal structure of ferric cyanide bound barley hexacoordina... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2oif | ||||||
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Title | The crystal structure of ferric cyanide bound barley hexacoordinate hemoglobin. | ||||||
Components | Non-legume hemoglobin | ||||||
Keywords | METAL BINDING PROTEIN / hexacoordinate hemoglobin / barley / ligand binding / non-symbiotic / symbiotic / evolution / conformational changes / oxygen transport | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Hordeum vulgare (barley) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 1.8 Å | ||||||
Authors | Hoy, J.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Plant hemoglobins: a molecular fossil record for the evolution of oxygen transport Authors: Hoy, J.A. / Robinson, H. / Trent III, J.T. / Kakar, S. / Smagghe, B.J. / Hargrove, M.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oif.cif.gz | 276.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oif.ent.gz | 225.7 KB | Display | PDB format |
PDBx/mmJSON format | 2oif.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2oif_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 2oif_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 2oif_validation.xml.gz | 60.3 KB | Display | |
Data in CIF | 2oif_validation.cif.gz | 81.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/2oif ftp://data.pdbj.org/pub/pdb/validation_reports/oi/2oif | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 18068.020 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hordeum vulgare (barley) / Gene: HB, GLB1 / Plasmid: pet29 / Production host: Escherichia coli (E. coli) / References: UniProt: Q42831 #2: Chemical | ChemComp-CYN / #3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-PGO / #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: 2.73 Å3/Da / Density % sol: 54.97 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.3 Details: 20% PEG 3350, 0.2 M ammonium citrate, 4% polypropylene glycol, 0.1 M sodium cyanide, 0.01 M hepes, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 1, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 141630 / Num. obs: 123785 / % possible obs: 87.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.045 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.378 / % possible all: 47.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.119 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.801→1.848 Å / Total num. of bins used: 20 /
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