+Open data
-Basic information
Entry | Database: PDB / ID: 1aby | ||||||
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Title | CYANOMET RHB1.1 (RECOMBINANT HEMOGLOBIN) | ||||||
Components | (HEMOGLOBIN) x 2 | ||||||
Keywords | OXYGEN TRANSPORT / HEME / RESPIRATORY PROTEIN / ERYTHROCYTE | ||||||
Function / homology | Function and homology information nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin 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 / platelet aggregation / hydrogen peroxide catabolic process / oxygen carrier activity / Late endosomal microautophagy / Heme signaling / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / response to hydrogen peroxide / Cytoprotection by HMOX1 / 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: 2.6 Å | ||||||
Authors | Kundrot, C.E. / Kroeger, K.S. | ||||||
Citation | Journal: Structure / Year: 1997 Title: Structures of a hemoglobin-based blood substitute: insights into the function of allosteric proteins. Authors: Kroeger, K.S. / Kundrot, C.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1aby.cif.gz | 125.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1aby.ent.gz | 99.3 KB | Display | PDB format |
PDBx/mmJSON format | 1aby.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1aby_validation.pdf.gz | 659.8 KB | Display | wwPDB validaton report |
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Full document | 1aby_full_validation.pdf.gz | 672.1 KB | Display | |
Data in XML | 1aby_validation.xml.gz | 14 KB | Display | |
Data in CIF | 1aby_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/1aby ftp://data.pdbj.org/pub/pdb/validation_reports/ab/1aby | 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: 30371.846 Da / Num. of mol.: 1 / Mutation: CHAIN A, V1M, CHAIN B, D, V1M, N108K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P69905 | ||||||||
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#2: Protein | Mass: 15937.343 Da / Num. of mol.: 2 / Mutation: CHAIN A, V1M, CHAIN B, D, V1M, N108K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P68871 #3: Chemical | ChemComp-CYN / #4: Chemical | ChemComp-HEM / #5: Water | ChemComp-HOH / | Compound details | HUMAN HEMOGLOBIN HAS TWO ALPHA CHAINS WHICH ARE CALLED CHAINS A AND C IN OTHER PDB FILES. IN THIS ...HUMAN HEMOGLOBIN | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.24 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5 / Details: pH 5.0 | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: May 1, 1995 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→115 Å / Num. obs: 19521 / % possible obs: 68.8 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.056 |
Reflection shell | Resolution: 2.6→2.8 Å / % possible all: 29.2 |
Reflection | *PLUS Num. measured all: 55634 |
Reflection shell | *PLUS % possible obs: 29.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY BML-3260 Resolution: 2.6→10 Å / Rfactor Rfree error: 0.0069 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 27.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.72 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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