+Open data
-Basic information
Entry | Database: PDB / ID: 1j7y | ||||||
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Title | Crystal structure of partially ligated mutant of HbA | ||||||
Components | (Hemoglobin) x 2 | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / globin / 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 / oxygen carrier activity / Late endosomal microautophagy / Heme signaling / response to hydrogen peroxide / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / 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 / 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 / FOURIER SYNTHESIS / Resolution: 1.7 Å | ||||||
Authors | Miele, A.E. / Draghi, F. / Arcovito, A. / Bellelli, A. / Brunori, M. / Travaglini-Allocatelli, C. / Vallone, B. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Control of heme reactivity by diffusion: structural basis and functional characterization in hemoglobin mutants. Authors: Miele, A.E. / Draghi, F. / Arcovito, A. / Bellelli, A. / Brunori, M. / Travaglini-Allocatelli, C. / Vallone, B. #1: Journal: J.Mol.Biol. / Year: 1999 Title: Modulation of Ligand Binding in Engineered Human Hemoglobin Distal Pocket Authors: Miele, A.E. / Santanche, S. / Travaglini-Allocatelli, C. / Vallone, B. / Brunori, M. / Bellelli, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j7y.cif.gz | 135.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j7y.ent.gz | 105.4 KB | Display | PDB format |
PDBx/mmJSON format | 1j7y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/1j7y ftp://data.pdbj.org/pub/pdb/validation_reports/j7/1j7y | HTTPS FTP |
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-Related structure data
Related structure data | 1j7sC 1j7wC 1qi8S 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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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 15222.417 Da / Num. of mol.: 2 / Fragment: alpha chain / Mutation: V1M, L29Y, H54Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HBA HUMAN / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): Tb-1 / References: UniProt: P69905 #2: Protein | Mass: 15962.263 Da / Num. of mol.: 2 / Fragment: beta chain / Mutation: V1M, L28Y, H63Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HBB HUMAN / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): Tb-1 / References: UniProt: P68871 |
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-Non-polymers , 4 types, 448 molecules
#3: Chemical | ChemComp-HEM / #4: Chemical | #5: Chemical | #6: 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: 43.79 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: small tubes / pH: 6.7 Details: ammonium sulphate, ammonium phosphate, pH 6.7, SMALL TUBES, temperature 298.0K | ||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 / Method: batch method / Details: Perutz, M.F., (1968) J.Crystal Growth, 2, 54. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 1, 2001 |
Radiation | Monochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→15 Å / Num. all: 56483 / Num. obs: 56483 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 30.1 |
Reflection shell | Highest resolution: 1.7 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.131 / % possible all: 93.8 |
Reflection | *PLUS Lowest resolution: 30 Å / % possible obs: 99.8 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.043 |
Reflection shell | *PLUS % possible obs: 98.5 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1QI8 Resolution: 1.7→14.9 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 24.03 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→14.9 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Rfactor obs: 0.155 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_angle_d / Dev ideal: 0.05 |