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Yorodumi- PDB-1jzl: Crystal structure of Sapharca inaequivalvis HbI, I114M mutant lig... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jzl | ||||||
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Title | Crystal structure of Sapharca inaequivalvis HbI, I114M mutant ligated to carbon monoxide. | ||||||
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 / 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: 1.5 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 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 | 1jzl.cif.gz | 73.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jzl.ent.gz | 54.2 KB | Display | PDB format |
PDBx/mmJSON format | 1jzl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jz/1jzl ftp://data.pdbj.org/pub/pdb/validation_reports/jz/1jzl | HTTPS FTP |
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-Related structure data
Related structure data | 1jwnC 1jzkC 1jzmC 3sdhS 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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Unit cell |
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Details | The biological assembly is a dimer formed from the A and B subunits of the assemetric unit. |
-Components
#1: Protein | Mass: 15984.356 Da / Num. of mol.: 2 / Mutation: I114M 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 | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.69 % |
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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 |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.5→40 Å / Num. all: 46282 / Num. obs: 40783 / % possible obs: 88.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 12.6 | ||||||||||||||||||
Reflection shell | Resolution: 1.5→1.55 Å / Rmerge(I) obs: 0.235 / Num. unique all: 1842 / % possible all: 39.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3SDH Resolution: 1.5→28.62 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1139634.69 / 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: 56.3873 Å2 / ksol: 0.382028 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→28.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.55 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
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Xplor file |
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