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Yorodumi- PDB-3aq9: Crystal structure of truncated hemoglobin from Tetrahymena pyrifo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3aq9 | ||||||
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Title | Crystal structure of truncated hemoglobin from Tetrahymena pyriformis, Q50E mutant, Fe(III) form | ||||||
Components | Group 1 truncated hemoglobin | ||||||
Keywords | OXYGEN BINDING / 2/2 fold hemoglobin / nitric oxide detoxification | ||||||
Function / homology | Function and homology information oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Tetrahymena pyriformis (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | ||||||
Authors | Igarashi, J. / Kobayashi, K. / Matsuoka, A. | ||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 2011 Title: A hydrogen-bonding network formed by the B10-E7-E11 residues of a truncated hemoglobin from Tetrahymena pyriformis is critical for stability of bound oxygen and nitric oxide detoxification. Authors: Igarashi, J. / Kobayashi, K. / Matsuoka, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3aq9.cif.gz | 116.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3aq9.ent.gz | 92.4 KB | Display | PDB format |
PDBx/mmJSON format | 3aq9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3aq9_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 3aq9_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3aq9_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 3aq9_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/3aq9 ftp://data.pdbj.org/pub/pdb/validation_reports/aq/3aq9 | HTTPS FTP |
-Related structure data
Related structure data | 3aq5SC 3aq6C 3aq7C 3aq8C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13707.839 Da / Num. of mol.: 2 / Mutation: Q50E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tetrahymena pyriformis (eukaryote) / Plasmid: pET-21c(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon Plus RIL / References: UniProt: P17724 #2: Chemical | #3: 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: 4.43 Å3/Da / Density % sol: 72.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2.0M ammonium citrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Oct 14, 2007 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→50 Å / Num. all: 52931 / Num. obs: 52931 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 1.74→1.77 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 3 / Rsym value: 0.27 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3AQ5 Resolution: 1.74→45.64 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.193 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.076 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.449 Å2
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Refinement step | Cycle: LAST / Resolution: 1.74→45.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.74→1.785 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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