+Open data
-Basic information
Entry | Database: PDB / ID: 1bz1 | ||||||
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Title | HEMOGLOBIN (ALPHA + MET) VARIANT | ||||||
Components |
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Keywords | OXYGEN STORAGE/TRANSPORT / OXYGEN TRANSPORT / 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 / OTHER / Resolution: 1.59 Å | ||||||
Authors | Kavanaugh, J.S. / Arnone, A. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Structural and functional properties of human hemoglobins reassembled after synthesis in Escherichia coli. Authors: Hui, H.L. / Kavanaugh, J.S. / Doyle, M.L. / Wierzba, A. / Rogers, P.H. / Arnone, A. / Holt, J.M. / Ackers, G.K. / Noble, R.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bz1.cif.gz | 127.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bz1.ent.gz | 101.2 KB | Display | PDB format |
PDBx/mmJSON format | 1bz1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/1bz1 ftp://data.pdbj.org/pub/pdb/validation_reports/bz/1bz1 | HTTPS FTP |
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-Related 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: 15281.550 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: SYNTHETIC ALPHA GLOBIN GENE; / Cell: RED BLOOD CELL / Gene: HUMAN ALPHA GLOBIN / Gene (production host): HUMAN ALPHA GLOBIN / Production host: Escherichia coli (E. coli) / References: UniProt: P69905 #2: Protein | Mass: 15890.198 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: SYNTHETIC ALPHA GLOBIN GENE / Cell: RED BLOOD CELL / Gene: HUMAN ALPHA GLOBIN / Gene (production host): HUMAN ALPHA GLOBIN / Production host: Escherichia coli (E. coli) / 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: 2.19 Å3/Da / Density % sol: 44 % Description: HBA STRUCTURE IN PDB SUBMISSION BNL- WAS USED AS THE STARTING MODEL FOR RIGID BODY REFINEMENT WITH X-PLOR FOLLOWED BY 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 | *PLUS |
Crystal grow | *PLUS Method: microdialysis |
Components of the solutions | *PLUS Conc.: 10 mM / Common name: ammonium phosphate |
-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: Sep 18, 1992 |
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: 1.59→25 Å / Num. obs: 61802 / % possible obs: 83.9 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.0528 / Rsym value: 0.0528 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.59→1.72 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 2.48 / Rsym value: 0.1962 / % possible all: 66.6 |
Reflection | *PLUS Num. measured all: 399325 |
Reflection shell | *PLUS % possible obs: 66.6 % |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: HBA STRUCTURE, PDB FILE IN BNL-25483 Resolution: 1.59→8 Å / Cross valid method: THROUGHOUT / σ(F): 2 Details: THE STARTING MODEL FOR REFINEMENT WAS THE HBA STRUCTURE IN PDB SUBMISSION BNL- 25483. RIGID BODY REFINEMENT WITH X-PLOR WAS FOLLOWED BY LEAST-SQUARES REFINEMENT WITH PROLSQ
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Displacement parameters | Biso mean: 20.89 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.59→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: 9.2 % / Rfactor obs: 0.17 / Rfactor Rwork: 0.17 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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