+Open data
-Basic information
Entry | Database: PDB / ID: 1qi8 | ||||||
---|---|---|---|---|---|---|---|
Title | DEOXYGENATED STRUCTURE OF A DISTAL POCKET HEMOGLOBIN MUTANT | ||||||
Components | (HEMOGLOBIN) x 2 | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / HEMOGLOBIN / BLOOD SUBSTITUTE / LOW NO REACTIVITY / 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: 1.8 Å | ||||||
Authors | Miele, A.E. / Vallone, B. / Santanche, S. / Travaglini-Allocatelli, C. / Bellelli, A. / Brunori, M. | ||||||
Citation | 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1qi8.cif.gz | 129.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1qi8.ent.gz | 101.6 KB | Display | PDB format |
PDBx/mmJSON format | 1qi8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/1qi8 ftp://data.pdbj.org/pub/pdb/validation_reports/qi/1qi8 | HTTPS FTP |
---|
-Related structure data
Related structure data | 2hhbS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 15222.417 Da / Num. of mol.: 2 / Fragment: ALPHA CHAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Cell: ERYTHROCYTE / Cellular location: CYTOPLASM / Plasmid: PKK223,3 / Cellular location (production host): CYTOPLASM / 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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Cell: ERYTHROCYTE / Cellular location: CYTOPLASM / Plasmid: PKK223,3 / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): TB-1 / References: UniProt: P68871 #3: Chemical | ChemComp-HEM / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 36.7 % |
---|---|
Crystal grow | pH: 6.5 / Details: HIGH SALT (PERUTZ, 1968)., pH 6.5 |
Crystal grow | *PLUS Details: refer to Perutz, M.F., (1968) J. Cryst. Growth, 2, 54. |
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Feb 1, 1999 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 42464 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 4.12 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.197 / % possible all: 64.4 |
Reflection | *PLUS Num. measured all: 51582 |
Reflection shell | *PLUS % possible obs: 64.4 % |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: OTHER Starting model: 2HHB Resolution: 1.8→16 Å / Cross valid method: THROUGHOUT / σ(F): 0
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→16 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|