+Open data
-Basic information
Entry | Database: PDB / ID: 2auq | ||||||
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Title | HbI (F97V) CO bound | ||||||
Components | Globin I | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / Allostery / Oxygen binding / hemoglobin / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information oxygen carrier activity / oxygen binding / heme binding / identical protein binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Scapharca inaequivalvis (ark clam) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Knapp, J.E. / Bonham, M.A. / Gibson, Q.H. / Nichols, J.C. / Royer Jr., W.E. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Residue F4 plays a key role in modulating oxygen affinity and cooperativity in Scapharca dimeric hemoglobin Authors: Knapp, J.E. / Bonham, M.A. / Gibson, Q.H. / Nichols, J.C. / Royer Jr., W.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2auq.cif.gz | 75 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2auq.ent.gz | 55.7 KB | Display | PDB format |
PDBx/mmJSON format | 2auq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/2auq ftp://data.pdbj.org/pub/pdb/validation_reports/au/2auq | HTTPS FTP |
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-Related structure data
Related structure data | 2auoC 2aupC 2aurC 2av0C 2av3C 3sdhS 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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1 |
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Unit cell |
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Details | The A and B chains form a molecular dimer as observed in solution. |
-Components
#1: Protein | Mass: 15919.261 Da / Num. of mol.: 2 / Mutation: F97V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Scapharca inaequivalvis (ark clam) / Plasmid: pcs-26 / Production host: Escherichia coli (E. coli) / Strain (production host): W3110lacIq L8 / References: UniProt: P02213 #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: 2.06 Å3/Da / Density % sol: 39.8 % |
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Crystal grow | Temperature: 298 K / Method: small tubes / pH: 7.5 / Details: Phosphate, pH 7.5, SMALL TUBES, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 2, 2000 / Details: Yale Mirrors |
Radiation | Monochromator: Yale Mirrors / 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→22.6 Å / Num. all: 26801 / Num. obs: 22915 / % possible obs: 85.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.158 / Mean I/σ(I) obs: 4.9 / Rsym value: 0.158 / % possible all: 68.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3SDH Resolution: 1.8→22.59 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1176328.11 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.2577 Å2 / ksol: 0.3472 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→22.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 10
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Xplor file |
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