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Yorodumi- PDB-3wct: The structure of a deoxygenated 400 kda hemoglobin provides a mor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wct | |||||||||
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Title | The structure of a deoxygenated 400 kda hemoglobin provides a more accurate description of the cooperative mechanism of giant hemoglobins: Oxygenated form | |||||||||
Components |
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Keywords | OXYGEN TRANSPORT / globin fold / oxygen binding / blood | |||||||||
Function / homology | Function and homology information hemoglobin complex / oxygen carrier activity / oxygen binding / response to hypoxia / iron ion binding / heme binding / extracellular region Similarity search - Function | |||||||||
Biological species | Lamellibrachia satsuma (invertebrata) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Numoto, N. / Nakagawa, T. / Ohara, R. / Hasegawa, T. / Kita, A. / Yoshida, T. / Maruyama, T. / Imai, K. / Fukumori, Y. / Miki, K. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: The structure of a deoxygenated 400 kDa haemoglobin reveals ternary- and quaternary-structural changes of giant haemoglobins Authors: Numoto, N. / Nakagawa, T. / Ohara, R. / Hasegawa, T. / Kita, A. / Yoshida, T. / Maruyama, T. / Imai, K. / Fukumori, Y. / Miki, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wct.cif.gz | 249.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wct.ent.gz | 202.6 KB | Display | PDB format |
PDBx/mmJSON format | 3wct.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wc/3wct ftp://data.pdbj.org/pub/pdb/validation_reports/wc/3wct | HTTPS FTP |
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-Related structure data
Related structure data | 3wcuC 3wcvC 3wcwC 1yhuS 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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1 |
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Unit cell |
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-Components
-Protein , 4 types, 8 molecules AEBFCGDH
#1: Protein | Mass: 16368.704 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lamellibrachia satsuma (invertebrata) / Tissue: blood / References: UniProt: S0BBU7 #2: Protein | Mass: 15951.922 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lamellibrachia satsuma (invertebrata) / Tissue: blood / References: UniProt: S0BBR6 #3: Protein | Mass: 16519.531 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lamellibrachia satsuma (invertebrata) / Tissue: blood / References: UniProt: S0BCU7 #4: Protein | Mass: 16228.627 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lamellibrachia satsuma (invertebrata) / Tissue: blood / References: UniProt: S0BAP9 |
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-Sugars , 1 types, 2 molecules
#5: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 4 types, 170 molecules
#6: Chemical | ChemComp-HEM / #7: Chemical | ChemComp-OXY / #8: Chemical | #9: 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: 2.53 Å3/Da / Density % sol: 51.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 13-18% PEG 3350, 0-5mM Ca acetate/Mg acetate, 100mM HEPES-NaOH, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Jul 6, 2009 |
Radiation | Monochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 50516 / Num. obs: 50516 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.7 % / Biso Wilson estimate: 34.9 Å2 / Rsym value: 0.086 / Net I/σ(I): 28.6 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 6.7 / Num. unique all: 5034 / Rsym value: 0.423 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YHU Resolution: 2.4→43.02 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3144448.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 25.9273 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→43.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.49 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10
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Xplor file |
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