+Open data
-Basic information
Entry | Database: PDB / ID: 1gzx | |||||||||
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Title | Oxy T State Haemoglobin - Oxygen bound at all four haems | |||||||||
Components |
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Keywords | OXYGEN TRANSPORT / HAEM PROTEIN / OXYGEN BINDING / TRANSPORT / COOPERATIVITY | |||||||||
Function / homology | Function and homology information nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin 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 / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / 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 / blood microparticle / ficolin-1-rich granule lumen / 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Paoli, M. / Liddington, R. / Tame, J. / Wilkinson, A. / Dodson, G. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1996 Title: Crystal Structure of T State Haemoglobin with Oxygen Bound at All Four Haems. Authors: Paoli, M. / Liddington, R. / Tame, J. / Wilkinson, A. / Dodson, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gzx.cif.gz | 134.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gzx.ent.gz | 103.1 KB | Display | PDB format |
PDBx/mmJSON format | 1gzx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/1gzx ftp://data.pdbj.org/pub/pdb/validation_reports/gz/1gzx | HTTPS FTP |
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-Related structure data
Related structure data | 1hgaS 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
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: LIGANDED T STATE / Source: (natural) Homo sapiens (human) / Cell: RED BLOOD CELLS / Tissue: BLOOD / References: UniProt: P69905 #2: Protein | Mass: 15890.198 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: LIGANDED T STATE / Source: (natural) Homo sapiens (human) / Cell: RED BLOOD CELLS / Tissue: BLOOD / References: UniProt: P68871 #3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-OXY / #5: Water | ChemComp-HOH / | Compound details | OXYGEN TRANSPORT FROM LUNG TO VARIOUS PERIPHERAL | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 57.4 % | ||||||||||||||||||||||||
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Crystal grow | pH: 7.2 Details: BATCH CRYSTALLISATION, OXYHB (75-90 MG/ML) IN 50MM POTASSIUM PHOSPHATE (PH 7.2), 22-28% PEG 8000 AND A 5 MOLAR EXCESS OF THE ALLOSTERIC EFFECTOR IHP | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: batch method | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277.15 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 35441 / % possible obs: 95 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 2.1→2.25 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 2.3 / % possible all: 85 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. all: 160538 / % possible obs: 95 % / Num. measured all: 255870 / Rmerge(I) obs: 0.09 |
Reflection shell | *PLUS % possible obs: 85 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDN ENTRY 1HGA Resolution: 2.1→10 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Details: BOND LENGTHS (A) : 0.018,
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Refinement step | Cycle: LAST / Resolution: 2.1→10 Å
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Refinement | *PLUS Lowest resolution: 10 Å / Num. reflection obs: 35176 / Rfactor Rwork: 0.195 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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