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Yorodumi- PDB-7e98: Oxy-deoxy intermediate of 400 kDa giant hemoglobin at 21% oxygen ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7.0E+98 | |||||||||
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Title | Oxy-deoxy intermediate of 400 kDa giant hemoglobin at 21% oxygen saturation | |||||||||
Components |
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Keywords | OXYGEN TRANSPORT / allostery / structural change / microspectrometry / crystal processing. | |||||||||
Function / homology | Function and homology information hemoglobin complex / oxygen carrier activity / oxygen binding / iron ion binding / heme binding / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | Oligobrachia mashikoi (invertebrata) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Numoto, N. / Kawano, Y. / Okumura, H. / Baba, S. / Fukumori, Y. / Miki, K. / Ito, N. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Iucrj / Year: 2021 Title: Coarse snapshots of oxygen-dissociation intermediates of a giant hemoglobin elucidated by determining the oxygen saturation in individual subunits in the crystalline state. Authors: Numoto, N. / Kawano, Y. / Okumura, H. / Baba, S. / Fukumori, Y. / Miki, K. / Ito, N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7e98.cif.gz | 134.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e98.ent.gz | 101.2 KB | Display | PDB format |
PDBx/mmJSON format | 7e98.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/7e98 ftp://data.pdbj.org/pub/pdb/validation_reports/e9/7e98 | HTTPS FTP |
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-Related structure data
Related structure data | 7e96C 7e97C 7e99C 2zfoS 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 on special symmetry positions |
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-Components
-Extracellular giant hemoglobin major globin subunit ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 15188.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oligobrachia mashikoi (invertebrata) / References: UniProt: Q7M419 |
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#2: Protein | Mass: 15327.087 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oligobrachia mashikoi (invertebrata) / References: UniProt: Q7M413 |
#3: Protein | Mass: 15621.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oligobrachia mashikoi (invertebrata) / References: UniProt: Q7M418 |
-Protein , 1 types, 1 molecules D
#4: Protein | Mass: 14693.341 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oligobrachia mashikoi (invertebrata) / References: UniProt: B1Q3G1 |
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-Non-polymers , 4 types, 347 molecules
#5: Chemical | ChemComp-HEM / #6: Chemical | ChemComp-OXY / #7: Chemical | ChemComp-GOL / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.7 Å3/Da / Density % sol: 54.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 11-12 % (w/v) polyethylene glycol (PEG) 10,000, 10 mM CaCl2, 200 mM Tris-HCl pH 8.0 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 3, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 33753 / % possible obs: 99.7 % / Redundancy: 10.3 % / Biso Wilson estimate: 36.6 Å2 / CC1/2: 0.997 / Rsym value: 0.19 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.2→2.33 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5320 / CC1/2: 0.666 / Rsym value: 1.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZFO Resolution: 2.2→47.84 Å / SU ML: 0.2763 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.5921 / Stereochemistry target values: GeoStd + Monomer Library
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.59 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→47.84 Å
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Refine LS restraints |
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LS refinement shell |
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