+Open data
-Basic information
Entry | Database: PDB / ID: 1o1n | ||||||
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Title | Deoxy hemoglobin (A-GLYGLYGLY-C:V1M,L29W; B,D:V1M) | ||||||
Components |
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Keywords | OXYGEN STORAGE/TRANSPORT / HEME / OXYGEN DELIVERY VEHICLE / BLOOD SUBSTITUTE / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
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: 1.8 Å | ||||||
Authors | Brucker, E.A. | ||||||
Citation | #1: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Genetically Crosslinked Hemoglobin: A Structural Study Authors: Brucker, E.A. #2: Journal: NAT.BIOTECHNOL. / Year: 1998 Title: Rate of Reaction with Nitric Oxide Determines the Hypertensive Effect of Cell-Free Hemoglobin Authors: Doherty, D.H. / Doyle, M.P. / Curry, S.R. / Vali, R.J. / Fattor, T.J. / Olson, J.S. / Lemon, D.D. #3: Journal: Nature / Year: 1992 Title: A Human Recombinant Hemoglobin Designed for Use as a Blood Substitute Authors: Looker, D. / Abbot-Brown, D. / Cozart, P. / Durfee, S. / Hoffman, S. / Mathews, A.J. / Miller-Roehrich, J. / Shoemaker, S. / Trimble, S. / Fermi, G. / Komiyama, N.H. / Nagai, K. / Stetler, G.L. | ||||||
History |
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Remark 999 | SEQUENCE HUMAN HEMOGLOBIN HAS TWO ALPHA CHAINS WHICH ARE CALLED CHAINS A AND C IN OTHER PDB FILES. ...SEQUENCE HUMAN HEMOGLOBIN HAS TWO ALPHA CHAINS WHICH ARE CALLED CHAINS A AND C IN OTHER PDB FILES. IN THIS ENTRY THE C-TERMINUS OF THE ALPHA-1 CHAIN AND THE N-TERMINUS OF THE ALPHA-2 CHAIN ARE GENETICALLY LINKED BY THREE GLYCINE RESIDUES TO FORM ONE COVALENTLY LINKED POLYPEPTIDE CHAIN. THESE THREE RESIDUES ARE HIGHLY DISORDERED, I.E. NOT DEFINED IN ELECTRON DENSITY. ALSO, THE INITIAL RESIDUE OF THE ALPHA-2 CHAIN, JUST AFTER THE GLYCINE LINKER, IS THE NATIVE VALINE, NOT A METHIONINE. THE THREE GLYCINE LINKER IS NOT INCLUDED IN THESE COORDINATES. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o1n.cif.gz | 131.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o1n.ent.gz | 102.3 KB | Display | PDB format |
PDBx/mmJSON format | 1o1n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o1/1o1n ftp://data.pdbj.org/pub/pdb/validation_reports/o1/1o1n | HTTPS FTP |
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-Related structure data
Related structure data | 1c7bS 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: 30632.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell: RED BLOOD CELL / Production host: Escherichia coli (E. coli) / References: UniProt: P69905 | ||||
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#2: Protein | Mass: 15922.265 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell: RED BLOOD CELL / Production host: Escherichia coli (E. coli) / References: UniProt: P68871 #3: Chemical | ChemComp-HEM / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33.2 % |
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Crystal grow | pH: 6.5 / Details: pH 6.50 |
-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 15, 1998 / Details: COLLIMATOR |
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: 1.8→30 Å / Num. obs: 48004 / % possible obs: 94.2 % / Redundancy: 3.28 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.09 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 3.87 / % possible all: 89.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1C7B Resolution: 1.8→8 Å / Num. parameters: 19279 / Num. restraintsaints: 28975 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL. 91(1973) 201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 4805 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→8 Å
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Refine LS restraints |
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