+Open data
-Basic information
Entry | Database: PDB / ID: 1bz0 | ||||||
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Title | HEMOGLOBIN A (HUMAN, DEOXY, HIGH SALT) | ||||||
Components |
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Keywords | OXYGEN STORAGE/TRANSPORT / OXYGEN TRANSPORT / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / 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 / OTHER / Resolution: 1.5 Å | ||||||
Authors | Kavanaugh, J.S. / Arnone, A. | ||||||
Citation | Journal: Biochemistry / Year: 1993 Title: Accommodation of insertions in helices: the mutation in hemoglobin Catonsville (Pro 37 alpha-Glu-Thr 38 alpha) generates a 3(10)-->alpha bulge. Authors: Kavanaugh, J.S. / Moo-Penn, W.F. / Arnone, A. #1: Journal: J.Mol.Biol. / Year: 1984 Title: The Crystal Structure of Human Deoxyhaemoglobin at 1.74 A Resolution Authors: Fermi, G. / Perutz, M.F. / Shaanan, B. / Fourme, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bz0.cif.gz | 127.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bz0.ent.gz | 100.5 KB | Display | PDB format |
PDBx/mmJSON format | 1bz0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bz0_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 1bz0_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 1bz0_validation.xml.gz | 25.5 KB | Display | |
Data in CIF | 1bz0_validation.cif.gz | 34.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/1bz0 ftp://data.pdbj.org/pub/pdb/validation_reports/bz/1bz0 | HTTPS FTP |
-Related structure data
Related structure data | 2hhbS 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 / Source: (natural) Homo sapiens (human) / Cell: RED BLOOD CELL / References: UniProt: P69905 #2: Protein | Mass: 15890.198 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: RED BLOOD CELL / 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: 4 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 44 % Description: HBA STRUCTURE IN PDB ENTRY 2HHB WAS USED AS THE STARTING MODEL FOR LEAST- SQUARES REFINEMENT WITH PROLSQ. | ||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 2.3 M AMMONIUM SULFATE 0.3 M AMMONIUM PHOSPHATE PH 6.5 10 MM FERROUS CITRATE | ||||||||||||||||||||||||
Crystal grow | *PLUS 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: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Jun 27, 1990 |
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: 1.5→25 Å / Num. obs: 84641 / % possible obs: 95.8 % / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Rmerge(I) obs: 0.0521 / Rsym value: 0.0521 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.5→1.62 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 3.25 / Rsym value: 0.166 / % possible all: 80.1 |
Reflection | *PLUS Num. measured all: 828088 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: HBA STRUCTURE IN PDB FILE 2HHB Resolution: 1.5→8 Å / Cross valid method: APOSTERIORI / σ(F): 2 Details: THE STARTING MODEL FOR LEAST-SQUARES REFINEMENT WITH PROLSQ WAS THE HBA STRUCTURE IN PDB ENTRY 2HHB
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Displacement parameters | Biso mean: 20.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→8 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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