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Yorodumi- PDB-1b0b: HEMOGLOBIN I FROM THE CLAM LUCINA PECTINATA, CYANIDE COMPLEX AT 1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b0b | ||||||
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Title | HEMOGLOBIN I FROM THE CLAM LUCINA PECTINATA, CYANIDE COMPLEX AT 100 KELVIN | ||||||
Components | HEMOGLOBIN | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / HEMOPROTEIN / SULFIDE CARRIER / GLOBINS / OXYGEN TRANSPORT / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information hemoglobin complex / oxygen transport / oxygen binding / heme binding / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Lucina pectinata (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.43 Å | ||||||
Authors | Rosano, C. / Rizzi, M. / Ascenzi, P. / Bolognesi, M. | ||||||
Citation | Journal: Biophys.J. / Year: 1999 Title: Cyanide binding to Lucina pectinata hemoglobin I and to sperm whale myoglobin: an x-ray crystallographic study. Authors: Bolognesi, M. / Rosano, C. / Losso, R. / Borassi, A. / Rizzi, M. / Wittenberg, J.B. / Boffi, A. / Ascenzi, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b0b.cif.gz | 45.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b0b.ent.gz | 30.7 KB | Display | PDB format |
PDBx/mmJSON format | 1b0b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/1b0b ftp://data.pdbj.org/pub/pdb/validation_reports/b0/1b0b | HTTPS FTP |
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-Related 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: 14829.690 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Lucina pectinata (invertebrata) / References: UniProt: P41260 |
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#2: Chemical | ChemComp-CYN / |
#3: Chemical | ChemComp-HEM / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 57 % | |||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 4.8 / Method: vapor diffusion | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.98 |
Detector | Date: Jul 1, 1998 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→20 Å / Num. obs: 29097 / % possible obs: 92.3 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 9.1 |
Reflection | *PLUS Lowest resolution: 8 Å / Num. obs: 25336 / Redundancy: 3 % / Rmerge(I) obs: 0.051 |
-Processing
Software |
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Refinement | Resolution: 1.43→8 Å
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Refine analyze | Num. disordered residues: 8 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.43→8 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.118 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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