+Open data
-Basic information
Entry | Database: PDB / ID: 2aur | ||||||
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Title | F97V (no ligand bound) | ||||||
Components | Globin I | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / Allostery / Oxygen binding / Hemoglobin / Oxygen transport / 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: 2.3 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 | 2aur.cif.gz | 66.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2aur.ent.gz | 49.4 KB | Display | PDB format |
PDBx/mmJSON format | 2aur.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/2aur ftp://data.pdbj.org/pub/pdb/validation_reports/au/2aur | HTTPS FTP |
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-Related structure data
Related structure data | 2auoC 2aupC 2auqC 2av0C 2av3C 4sdhS 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 dimer, which is the biological unit |
-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: 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: 2.19 Å3/Da / Density % sol: 43.5 % |
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Crystal grow | Temperature: 298 K / Method: small tubes / pH: 8.5 / Details: Phosphate, pH 8.5, 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: Sep 29, 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: 2.3→30.7 Å / Num. all: 13482 / Num. obs: 11945 / % possible obs: 0.886 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.253 / % possible all: 78 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4SDH Resolution: 2.3→30.7 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2080291.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.6111 Å2 / ksol: 0.327939 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→30.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 10
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Xplor file |
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