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Yorodumi- PDB-2z8a: Ligand Migration and Binding in The Dimeric Hemoglobin of Scaphar... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z8a | ||||||
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Title | Ligand Migration and Binding in The Dimeric Hemoglobin of Scapharca Inaequivalvis: I25W with CO Bound to HEME and in the Presence of 3 Atoms of XE | ||||||
Components | Globin-1 | ||||||
Keywords | OXYGEN BINDING / OXYGEN TRANSPORT / ALLOSTERY / OXYGEN AFFINITY / Cytoplasm / Heme / Iron / Metal-binding / OXYGEN STORAGE/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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 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 | 2z8a.cif.gz | 147.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z8a.ent.gz | 114 KB | Display | PDB format |
PDBx/mmJSON format | 2z8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2z8a_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2z8a_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2z8a_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 2z8a_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z8/2z8a ftp://data.pdbj.org/pub/pdb/validation_reports/z8/2z8a | HTTPS FTP |
-Related structure data
Related structure data | 2r4wC 2r4xC 2r4yC 2r4zC 2z85C 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 on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 16040.356 Da / Num. of mol.: 2 / Mutation: I1025W/I2025W 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 |
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-Non-polymers , 5 types, 382 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-XE / #5: Chemical | ChemComp-PO4 / | #6: 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: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.06→46.3 Å / Num. obs: 118984 / % possible obs: 95.3 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 24.1 |
Reflection shell | Resolution: 1.06→1.1 Å / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 5.5 / Rsym value: 0.286 / % possible all: 90.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3SDH Resolution: 1.06→46.3 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE MODEL WAS REFINED WITH A COMBINATION OF CNS AND SHELX WITH A ROUND OF MANUAL INTERVENTION IN BETWEEN.
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Refinement step | Cycle: LAST / Resolution: 1.06→46.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.06→1.1 Å / Total num. of bins used: 10
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