+Open data
-Basic information
Entry | Database: PDB / ID: 1bij | ||||||
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Title | CROSSLINKED, DEOXY HUMAN HEMOGLOBIN A | ||||||
Components | (HEMOGLOBIN A) x 2 | ||||||
Keywords | OXYGEN TRANSPORT / HEME / ALLOSTERIC INTERMEDIATE / CROSSLINKED | ||||||
Function / homology | Function and homology information nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin 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 / 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 / oxygen binding / regulation of blood pressure / platelet aggregation / Chaperone Mediated Autophagy / peroxidase activity / 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: 2.3 Å | ||||||
Authors | Fernandez, E.J. / Abad-Zapatero, C. / Olsen, K.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Crystal structure of Lysbeta(1)82-Lysbeta(2)82 crosslinked hemoglobin: a possible allosteric intermediate Authors: Fernandez, E.J. / Abad-Zapatero, C. / Olsen, K.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bij.cif.gz | 122 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bij.ent.gz | 100.3 KB | Display | PDB format |
PDBx/mmJSON format | 1bij.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bij_validation.pdf.gz | 685.3 KB | Display | wwPDB validaton report |
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Full document | 1bij_full_validation.pdf.gz | 709.3 KB | Display | |
Data in XML | 1bij_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 1bij_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/1bij ftp://data.pdbj.org/pub/pdb/validation_reports/bi/1bij | HTTPS FTP |
-Related structure data
Related structure data | 1hhb 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: LYS B82/D82 CROSSLINKED HEMOGLOBIN / Source: (natural) Homo sapiens (human) / References: UniProt: P69905 #2: Protein | Mass: 15890.198 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: LYS B82/D82 CROSSLINKED HEMOGLOBIN / Source: (natural) Homo sapiens (human) / References: UniProt: P68871 #3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-2FU / | #5: 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: 2.4 Å3/Da | |||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | |||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.1 / Method: batch method | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jul 1, 1993 |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 53187 / % possible obs: 73 % / Observed criterion σ(I): 2.5 / Redundancy: 2.5 % / Rmerge(I) obs: 0.111 / Rsym value: 0.0394 / Net I/σ(I): 2.02 |
Reflection shell | Resolution: 2.25→2.81 Å / % possible all: 73.1 |
Reflection | *PLUS Lowest resolution: 53.2 Å / Rmerge(I) obs: 0.0397 |
Reflection shell | *PLUS % possible obs: 73.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HHB 1hhb Resolution: 2.3→5 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2.5
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→5 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |