+Open data
-Basic information
Entry | Database: PDB / ID: 1it3 | ||||||
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Title | Hagfish CO ligand hemoglobin | ||||||
Components | hemoglobin | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / hagfish / Eptatretus burgeri / CO form / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information oxygen carrier activity / oxygen binding / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Eptatretus burgeri (inshore hagfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Mito, M. / Chong, K.T. / Park, S.-Y. / Tame, J.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Crystal structures of deoxy- and carbonmonoxyhemoglobin F1 from the hagfish Eptatretus burgeri Authors: Mito, M. / Chong, K.T. / Miyazaki, G. / Adachi, S. / Park, S.-Y. / Tame, J.R. / Morimoto, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1it3.cif.gz | 140.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1it3.ent.gz | 109 KB | Display | PDB format |
PDBx/mmJSON format | 1it3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/it/1it3 ftp://data.pdbj.org/pub/pdb/validation_reports/it/1it3 | HTTPS FTP |
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-Related structure data
Related structure data | 1it2C 1f5oS 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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Unit cell |
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-Components
#1: Protein | Mass: 16864.525 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Eptatretus burgeri (inshore hagfish) / References: UniProt: Q7SID0 #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: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.83 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: small tubes / pH: 6.5 Details: PEG 4000, Tris-Buffer, pH 6.5, SMALL TUBES, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 27 ℃ / Method: batch method | |||||||||||||||||||||||||||||||||||||||||||||||||
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: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 23, 2000 / Details: mirrors |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 73549 / Num. obs: 32410 / % possible obs: 84.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.181 / % possible all: 63.9 |
Reflection | *PLUS % possible obs: 83.2 % / Num. measured all: 73549 / Rmerge(I) obs: 0.07 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1F5O Resolution: 2.1→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.021
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5.06 % / Rfactor obs: 0.195 / Rfactor Rfree: 0.283 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.1 Å / Rfactor Rfree: 0.303 / Rfactor Rwork: 0.272 |