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Yorodumi- PDB-2r4z: Ligand Migration and Binding in The Dimeric Hemoglobin of Scaphar... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r4z | ||||||
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Title | Ligand Migration and Binding in The Dimeric Hemoglobin of Scapharca Inaequivalvis: Structure of I25W with CO | ||||||
Components | Globin-1 | ||||||
Keywords | OXYGEN BINDING / OXYGEN TRANSPORT / ALLOSTERY / OXYGEN AFFINITY / OXYGEN STORAGE/TRANSPORT / Cytoplasm / Heme / Iron / Metal-binding | ||||||
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: 1.6 Å | ||||||
Authors | Knapp, J.E. / Royer Jr., W.E. / Nienhaus, K. / Palladino, P. / Nienhaus, G.U. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Ligand Migration and Binding in the Dimeric Hemoglobin of Scapharca inaequivalvis Authors: Nienhaus, K. / Knapp, J.E. / Palladino, P. / Royer Jr., W.E. / Nienhaus, G.U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r4z.cif.gz | 80.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r4z.ent.gz | 59.2 KB | Display | PDB format |
PDBx/mmJSON format | 2r4z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/2r4z ftp://data.pdbj.org/pub/pdb/validation_reports/r4/2r4z | HTTPS FTP |
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-Related structure data
Related structure data | 2r4wC 2r4xC 2r4yC 2z85C 2z8aC 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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-Components
#1: Protein | Mass: 16040.356 Da / Num. of mol.: 2 / Mutation: I25W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Scapharca inaequivalvis (ark clam) / Gene: HBI / Plasmid: PCS-26 / Production host: Escherichia coli (E. coli) / Strain (production host): W3110LACIQL8 / References: UniProt: P02213 #2: Chemical | ChemComp-PO4 / | #3: Chemical | #4: Chemical | #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: 2.11 Å3/Da / Density % sol: 42 % |
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Crystal grow | Temperature: 298 K / Method: small tubes / pH: 7.5 Details: 1.5-2.5M PHOSPHATE BUFFER, pH 7.50, SMALL TUBES, temperature 298K |
-Data collection
Diffraction | Mean temperature: 110 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: Oct 4, 2003 / Details: OSMIC MIRRORS |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40 Å / Num. obs: 34377 / % possible obs: 93.4 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 4.4 / Rsym value: 0.256 / % possible all: 80.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3SDH Resolution: 1.6→29.77 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1050101.17 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.1884 Å2 / ksol: 0.3161 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 16.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→29.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.66 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 10
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Xplor file |
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