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Yorodumi- PDB-2r4x: Ligand Migration and Binding in The Dimeric Hemoglobin of Scaphar... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r4x | ||||||
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Title | Ligand Migration and Binding in The Dimeric Hemoglobin of Scapharca Inaequivalvis: H69V/I114M co complex | ||||||
Components | Globin-1 | ||||||
Keywords | OXYGEN BINDING / ALLOSTERY / OXYGEN AFFINITY / COOPERATIVE HEMOGLOBIN / OXYGEN STORAGE/TRANSPORT / Cytoplasm / Heme / Iron / Metal-binding / Oxygen transport | ||||||
Function / homology | Function and homology information oxygen carrier activity / oxygen binding / response to hypoxia / 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: 2.1 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 | 2r4x.cif.gz | 67.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r4x.ent.gz | 49.9 KB | Display | PDB format |
PDBx/mmJSON format | 2r4x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2r4x_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2r4x_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2r4x_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 2r4x_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/2r4x ftp://data.pdbj.org/pub/pdb/validation_reports/r4/2r4x | HTTPS FTP |
-Related structure data
Related structure data | 2r4wC 2r4yC 2r4zC 2z85C 2z8aC 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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-Components
#1: Protein | Mass: 15946.325 Da / Num. of mol.: 2 / Mutation: H69V/I114M 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 | #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: 2.2 Å3/Da / Density % sol: 45 % |
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Crystal grow | Temperature: 298 K / Method: small tubes / pH: 8.5 Details: 1.5-2.5M PHOSPHATE, pH 8.50, SMALL TUBES, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 25, 2005 / 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: 2.1→40 Å / Num. obs: 15743 / % possible obs: 88.7 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.242 / % possible all: 76 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4SDH Resolution: 2.1→33.24 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2142647.66 / 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: 59.2439 Å2 / ksol: 0.339666 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 26.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→33.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.18 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 10
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Xplor file |
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