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Yorodumi- PDB-2zs0: Structural Basis for the Heterotropic and Homotropic Interactions... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zs0 | ||||||
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Title | Structural Basis for the Heterotropic and Homotropic Interactions of Invertebrate Giant Hemoglobin | ||||||
Components | (Extracellular giant hemoglobin major globin subunit ...) x 4 | ||||||
Keywords | Oxygen Storage / Oxygen transport / hemoglobin / annelida / magnesium / cooperativity / Heme / Iron / Metal-binding / Secreted / Transport | ||||||
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 | Oligobrachia mashikoi (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Numoto, N. / Nakagawa, T. / Kita, A. / Sasayama, Y. / Fukumori, Y. / Miki, K. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Structural Basis for the Heterotropic and Homotropic Interactions of Invertebrate Giant Hemoglobin Authors: Numoto, N. / Nakagawa, T. / Kita, A. / Sasayama, Y. / Fukumori, Y. / Miki, K. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zs0.cif.gz | 151.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zs0.ent.gz | 116.2 KB | Display | PDB format |
PDBx/mmJSON format | 2zs0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zs0_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 2zs0_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 2zs0_validation.xml.gz | 33.4 KB | Display | |
Data in CIF | 2zs0_validation.cif.gz | 48.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/2zs0 ftp://data.pdbj.org/pub/pdb/validation_reports/zs/2zs0 | HTTPS FTP |
-Related structure data
Related structure data | 2zs1C 2d2mS 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 ... , 4 types, 4 molecules ABCD
#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 |
#4: Protein | Mass: 14693.341 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oligobrachia mashikoi (invertebrata) / References: UniProt: Q5KSB7 |
-Non-polymers , 6 types, 758 molecules
#5: Chemical | ChemComp-HEM / #6: Chemical | ChemComp-OXY / #7: Chemical | ChemComp-CA / #8: Chemical | ChemComp-CL / | #9: Chemical | #10: 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: 2.66 Å3/Da / Density % sol: 53.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 10% PEG 10000, 0.2M Tris-HCl pH 8.0, 10mM CaCl2, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Mar 11, 2007 / Details: vertically bent cylinder mirror coated in Rhodium |
Radiation | Monochromator: Fixed exit Si 111 double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 85070 / Num. obs: 85070 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 10.9 % / Biso Wilson estimate: 23 Å2 / Rsym value: 0.047 / Net I/σ(I): 38.6 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 6 / Num. unique all: 8433 / Rsym value: 0.37 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2D2M Resolution: 1.6→47.23 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3781672.56 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / 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: 49.834 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→47.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.66 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 10
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Xplor file |
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