+Open data
-Basic information
Entry | Database: PDB / ID: 1bzz | ||||||
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Title | HEMOGLOBIN (ALPHA V1M) MUTANT | ||||||
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 alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / hydrogen peroxide catabolic process / Late endosomal microautophagy / oxygen carrier activity / carbon dioxide transport / Heme signaling / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / regulation of blood pressure / platelet aggregation / oxygen binding / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / blood microparticle / ficolin-1-rich granule lumen / 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 | 1bzz.cif.gz | 128.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bzz.ent.gz | 100.8 KB | Display | PDB format |
PDBx/mmJSON format | 1bzz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/1bzz ftp://data.pdbj.org/pub/pdb/validation_reports/bz/1bzz | HTTPS FTP |
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-Related structure data
Related structure data | 1bz1C 1bz0S S: Starting model for refinement C: citing same article (ref.) |
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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: 15182.419 Da / Num. of mol.: 2 / Mutation: V1M 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 FILE 1BZ0 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: 7 Details: 2.3 M AMMONIUM SULFATE 0.3 M AMMONIUM PHOSPHATE PH 6.5 10 MM FERROUS CITRATE, pH 7.0 |
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 25, 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: 64636 / % possible obs: 88.7 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.0477 / Rsym value: 0.05477 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.59→1.72 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.1532 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.1532 / % possible all: 73.4 |
Reflection | *PLUS Num. measured all: 448711 |
Reflection shell | *PLUS % possible obs: 73.4 % |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: HBA STRUCTURE, PDB FILE 1BZ0. Resolution: 1.59→8 Å / Cross valid method: THROUGHOUT / σ(F): 2 Details: THE STARTING MODEL FOR REFINEMENT WAS THE HBA STRUCTURE IN PDB FILE 1BZ0. RIGID BODY REFINEMENT WITH X-PLOR WAS FOLLOWED BY LEAST-SQUARES REFINEMENT WITH PROLSQ
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Displacement parameters | Biso mean: 20.42 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: 10 % / Rfactor obs: 0.163 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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