+Open data
-Basic information
Entry | Database: PDB / ID: 1ebt | ||||||
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Title | HEMOGLOBIN I FROM THE CLAM LUCINA PECTINATA BOUND WITH CYANIDE | ||||||
Components | HEMOGLOBIN | ||||||
Keywords | OXYGEN TRANSPORT / HEMOGLOBIN / OXYGEN CARRIER / GLOBIN | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Rosano, C. / Bolognesi, M. / Ascenzi, P. | ||||||
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 | 1ebt.cif.gz | 37.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ebt.ent.gz | 28 KB | Display | PDB format |
PDBx/mmJSON format | 1ebt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/1ebt ftp://data.pdbj.org/pub/pdb/validation_reports/eb/1ebt | HTTPS FTP |
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-Related structure data
Related structure data | 1b0bC 1ebcC 1flpS 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
#1: Protein | Mass: 14744.429 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: 2.5 Å3/Da / Density % sol: 50.8 % | |||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.00 | |||||||||||||||
Crystal grow | *PLUS pH: 5.75 / Method: unknown | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Dec 1, 1995 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→24 Å / Num. obs: 12085 / % possible obs: 93 % / Redundancy: 2.2 % |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 24 Å / % possible obs: 93.3 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.054 |
Reflection shell | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 2 Å / Mean I/σ(I) obs: 5.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FLP Resolution: 1.9→24 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO /
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Solvent computation | Bsol: 57.8 Å2 / ksol: 0.84 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→24 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.184 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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