+Open data
-Basic information
Entry | Database: PDB / ID: 2av3 | |||||||||
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Title | F97L- no ligand | |||||||||
Components | Globin I | |||||||||
Keywords | OXYGEN STORAGE/TRANSPORT / Allosteric / oxygen binding / oxygen transport / 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: 1.7 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. #1: Journal: J.Biol.Chem. / Year: 1997 Title: Mutation of residue PHE97 to Leu disrupts the central allosteric pathway in Scapharca dimeric hemoglobin. Authors: Pardanani, A. / Gibson, Q.H. / Colotti, G. / 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 | 2av3.cif.gz | 73.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2av3.ent.gz | 54.1 KB | Display | PDB format |
PDBx/mmJSON format | 2av3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/2av3 ftp://data.pdbj.org/pub/pdb/validation_reports/av/2av3 | HTTPS FTP |
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-Related structure data
Related structure data | 2auoC 2aupC 2auqC 2aurC 2av0C 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 dimeric assembly that is the functional biological unit. |
-Components
#1: Protein | Mass: 15933.286 Da / Num. of mol.: 2 / Mutation: F97L 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: 2.1 Å3/Da / Density % sol: 41.1 % |
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Crystal grow | Temperature: 298 K / Method: small tubes / pH: 8.5 Details: Phosphate buffer, 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: Aug 14, 1995 / Details: Collimator |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→10 Å / Num. all: 32599 / Num. obs: 27416 / % possible obs: 84.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 |
Reflection shell | Resolution: 1.7→1.76 Å / % possible all: 69.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4SDH Resolution: 1.7→9.95 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1385052.92 / 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: 58.4121 Å2 / ksol: 0.345133 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→9.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.76 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 10
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Xplor file |
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