+Open data
-Basic information
Entry | Database: PDB / ID: 1a3o | ||||||
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Title | ARTIFICIAL MUTANT (ALPHA Y42H) OF DEOXY HEMOGLOBIN | ||||||
Components |
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Keywords | OXYGEN TRANSPORT / HEME / RESPIRATORY PROTEIN / ERYTHROCYTE | ||||||
Function / homology | Function and homology information nitric oxide transport / cellular oxidant detoxification / hemoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / cellular oxidant detoxification / hemoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / 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 / regulation of blood pressure / 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 / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / Factors involved in megakaryocyte development and platelet production / tertiary granule lumen / 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 / Resolution: 1.8 Å | ||||||
Authors | Tame, J. / Vallone, B. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: The structures of deoxy human haemoglobin and the mutant Hb Tyralpha42His at 120 K. Authors: Tame, J.R. / Vallone, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a3o.cif.gz | 131.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a3o.ent.gz | 103.7 KB | Display | PDB format |
PDBx/mmJSON format | 1a3o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a3o_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 1a3o_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 1a3o_validation.xml.gz | 28 KB | Display | |
Data in CIF | 1a3o_validation.cif.gz | 39.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/1a3o ftp://data.pdbj.org/pub/pdb/validation_reports/a3/1a3o | HTTPS FTP |
-Related 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: 15125.327 Da / Num. of mol.: 2 / Mutation: CHAIN A, C, Y42H / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: RED CELL / Tissue: BLOOD / References: UniProt: P69905 #2: Protein | Mass: 15890.198 Da / Num. of mol.: 2 / Mutation: CHAIN A, C, Y42H / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: RED CELL / Tissue: BLOOD / References: UniProt: P68871 #3: Chemical | ChemComp-HEM / #4: 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: 2.15 Å3/Da / Density % sol: 42.69 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.5 / Method: unknown / Details: Perutz, M.F., (1968) J. Cryst. Growth, 2, 54. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: May 1, 1997 / Details: MIRROR |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→15 Å / Num. obs: 49373 / % possible obs: 96.02 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.8→1.87 Å / Redundancy: 1.36 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 2.9 / % possible all: 74.2 |
Reflection shell | *PLUS % possible obs: 76.4 % |
-Processing
Software |
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Refinement | Resolution: 1.8→15 Å / σ(F): 0
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Displacement parameters | Biso mean: 21.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→15 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 45030 / Rfactor obs: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |