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Yorodumi- PDB-1jwn: Crystal Structure of Scapharca inaequivalvis HbI, I114F Mutant Li... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jwn | ||||||
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Title | Crystal Structure of Scapharca inaequivalvis HbI, I114F Mutant Ligated to Carbon Monoxide. | ||||||
Components | Globin I - Ark Shell | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / Invertebrate Hemoglobin / Allostery / Cooperativity / Oxygen-binding Protein / 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: 2.1 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 | 1jwn.cif.gz | 118.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jwn.ent.gz | 95.7 KB | Display | PDB format |
PDBx/mmJSON format | 1jwn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jwn_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 1jwn_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 1jwn_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | 1jwn_validation.cif.gz | 33 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jw/1jwn ftp://data.pdbj.org/pub/pdb/validation_reports/jw/1jwn | HTTPS FTP |
-Related 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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-Components
#1: Protein | Mass: 16000.335 Da / Num. of mol.: 4 / Mutation: YES 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): W3110LACIQ L8 / References: UniProt: P02213 #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-CMO / #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: 2.27 Å3/Da / Density % sol: 45.92 % | |||||||||||||||
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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 | |||||||||||||||
Crystal grow | *PLUS Method: batch method / Details: Royer Jr., W.E., (1994) J.Mol.Biol., 235, 657. | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Feb 13, 2000 / Details: mirrors | ||||||||||||||||||
Radiation |
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Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.1→40 Å / Num. all: 34151 / Num. obs: 30305 / % possible obs: 88.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.2 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 8.6 | ||||||||||||||||||
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 3.9 / Num. unique all: 2658 / % possible all: 78.5 | ||||||||||||||||||
Reflection | *PLUS Highest resolution: 2.1 Å / Num. obs: 30296 / Rmerge(I) obs: 0.092 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 78.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→29.5 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1065250.06 / 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: 50.5346 Å2 / ksol: 0.329872 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→29.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.18 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 30296 / σ(F): 0 / Num. reflection Rfree: 3036 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 21.6 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.281 / % reflection Rfree: 10.2 % / Rfactor Rwork: 0.229 |