+Open data
-Basic information
Entry | Database: PDB / ID: 1o1l | ||||||
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Title | Deoxy hemoglobin (A-GLY-C:V1M,L29W,H58Q; 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 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 / 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 TWO ALPHA CHAINS HAVE BEEN COVALENTLY JOINED TOGETHER BY ONE GLYCINE RESIDUE TO FORM ONE COVALENTLY LINKED POLYPEPTIDE CHAIN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o1l.cif.gz | 129.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o1l.ent.gz | 100.7 KB | Display | PDB format |
PDBx/mmJSON format | 1o1l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o1/1o1l ftp://data.pdbj.org/pub/pdb/validation_reports/o1/1o1l | HTTPS FTP |
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-Related structure data
Related structure data | 1c7cS 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: 30497.908 Da / Num. of mol.: 1 / Mutation: V1M, L29W, H58Q 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 / Mutation: V1M 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: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33.3 % |
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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: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 15, 2000 / Details: OSMIC CONFOCAL MAXFLUX |
Radiation | 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: 47994 / % possible obs: 94.2 % / Redundancy: 2.771 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 2.66 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 6.1 / % possible all: 91.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1C7C Resolution: 1.8→8 Å / Num. parameters: 18995 / Num. restraintsaints: 23106 / 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: 4743 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→8 Å
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Refine LS restraints |
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