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Yorodumi- PDB-1jzk: Crystal Structure of Scapharca inaequivalvis HbI, I114F mutant (deoxy) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jzk | ||||||
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Title | Crystal Structure of Scapharca inaequivalvis HbI, I114F mutant (deoxy) | ||||||
Components | GLOBIN I - ARK SHELL | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / invertebrate / hemoglobin / allostery / cooperativity / oxygen-binding / oxygen-transport / heme protein / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
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: 2.2 Å | ||||||
Authors | Knapp, J.E. / Gibson, Q.H. / Cushing, L. / Royer Jr., W.E. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Restricting the Ligand-Linked Heme Movement in Scapharca Dimeric Hemoglobin Reveals Tight Coupling between Distal and Proximal Contributions to Cooperativity. Authors: Knapp, J.E. / Gibson, Q.H. / Cushing, L. / 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. #2: Journal: J.Mol.Biol. / Year: 1994 Title: High Resolution Crystallographic Analysis of a Co-operative Dimeric Hemoglobin. Authors: 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 | 1jzk.cif.gz | 119.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jzk.ent.gz | 96.5 KB | Display | PDB format |
PDBx/mmJSON format | 1jzk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jzk_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 1jzk_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 1jzk_validation.xml.gz | 26 KB | Display | |
Data in CIF | 1jzk_validation.cif.gz | 35 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jz/1jzk ftp://data.pdbj.org/pub/pdb/validation_reports/jz/1jzk | HTTPS FTP |
-Related structure data
Related structure data | 1jwnC 1jzlC 1jzmC 4sdhS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological assembly is either the AB dimer or the CD dimer found in the assemetric unit. |
-Components
#1: Protein | Mass: 16000.335 Da / Num. of mol.: 4 / Mutation: I114F 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): W3110LACIQL8 / References: UniProt: P02213 #2: Chemical | ChemComp-HEM / #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: 2.27 Å3/Da / Density % sol: 45.93 % |
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Crystal grow | Temperature: 296 K / Method: microbatch / pH: 7.5 Details: 2.1-2.3M Phosphate buffer, pH 7.5, Microbatch, temperature 296K |
-Data collection
Diffraction | Mean temperature: 296 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: Feb 23, 2001 / Details: 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: 2.2→40 Å / Num. all: 29156 / Num. obs: 28828 / % possible obs: 97.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.173 / % possible all: 81.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4SDH Resolution: 2.2→37.69 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1409034.45 / 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: 36.7878 Å2 / ksol: 0.333933 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→37.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
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Xplor file |
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