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Yorodumi- PDB-2d60: Crystal structure of deoxy human hemoglobin complexed with two L3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d60 | ||||||
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Title | Crystal structure of deoxy human hemoglobin complexed with two L35 molecules | ||||||
Components |
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Keywords | OXYGEN STORAGE/TRANSPORT / HEMOGLOBIN / L35 / ALLOSTERIC EFFECTOR / CRYSTAL SRUCTURE / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information cellular oxidant detoxification / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / hemoglobin binding / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...cellular oxidant detoxification / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / hemoglobin binding / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / hydrogen peroxide catabolic process / oxygen carrier activity / Late endosomal microautophagy / Heme signaling / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / response to hydrogen peroxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / platelet aggregation / oxygen binding / regulation of blood pressure / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / ficolin-1-rich granule lumen / blood microparticle / iron ion binding / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Yokoyama, T. / Neya, S. / Tsuneshige, A. / Yonetani, T. / Park, S.Y. / Tame, J.R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: R-state haemoglobin with low oxygen affinity: crystal structures of deoxy human and carbonmonoxy horse haemoglobin bound to the effector molecule L35 Authors: Yokoyama, T. / Neya, S. / Tsuneshige, A. / Yonetani, T. / Park, S.Y. / Tame, J.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d60.cif.gz | 127.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d60.ent.gz | 101.2 KB | Display | PDB format |
PDBx/mmJSON format | 2d60.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/2d60 ftp://data.pdbj.org/pub/pdb/validation_reports/d6/2d60 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Biological unit is a tetramer same as asymmetric unit |
-Components
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: red cell / References: UniProt: P69905 #2: Protein | Mass: 15890.198 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: red cell / References: UniProt: P68871 #3: Chemical | ChemComp-HEM / #4: Chemical | #5: 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: 2.16 Å3/Da / Density % sol: 42.98 % |
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Crystal grow | Temperature: 293 K / Method: batch / pH: 6.5 Details: 2.5M Ammonium sulfate, Ammonium phosphate, 0.1mM L35, pH 6.5, BATCH, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. obs: 49000 / % possible obs: 85.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.45 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.258 / % possible all: 63.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→19.88 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.203 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.804 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→19.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.703→1.747 Å / Total num. of bins used: 20 /
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