+Open data
-Basic information
Entry | Database: PDB / ID: 1a0z | ||||||
---|---|---|---|---|---|---|---|
Title | HEMOGLOBIN (VAL BETA1 MET) MUTANT | ||||||
Components |
| ||||||
Keywords | OXYGEN TRANSPORT | ||||||
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 / ISOMORPHOUS WITH DEOXYHEMOGLOBIN A / Resolution: 2 Å | ||||||
Authors | Kavanaugh, J.S. / Arnone, A. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: High-resolution crystal structures of human hemoglobin with mutations at tryptophan 37beta: structural basis for a high-affinity T-state,. Authors: Kavanaugh, J.S. / Weydert, J.A. / Rogers, P.H. / Arnone, A. #1: Journal: Biochemistry / Year: 1992 Title: High-Resolution X-Ray Study of Deoxyhemoglobin Rothschild 37 Beta Trp-->Arg: A Mutation that Creates an Intersubunit Chloride-Binding Site Authors: Kavanaugh, J.S. / Rogers, P.H. / Case, D.A. / Arnone, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1a0z.cif.gz | 128.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1a0z.ent.gz | 101.9 KB | Display | PDB format |
PDBx/mmJSON format | 1a0z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/1a0z ftp://data.pdbj.org/pub/pdb/validation_reports/a0/1a0z | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.94917, -0.05084, 0.31063), Vector: |
-Components
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell: RED BLOOD CELL / Gene: HUMAN BETA GLOBIN / Organ: BLOOD / Gene (production host): HUMAN BETA GLOBIN / Production host: Escherichia coli (E. coli) / References: UniProt: P69905 #2: Protein | Mass: 15922.265 Da / Num. of mol.: 2 / Mutation: V1M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell: RED BLOOD CELL / Gene: HUMAN BETA GLOBIN / Organ: BLOOD / Gene (production host): HUMAN BETA GLOBIN / Production host: Escherichia coli (E. coli) / 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: 2.32 Å3/Da / Density % sol: 47 % Description: DEOXYHEMOGLOBIN A IN THE SAME CELL WAS USED AS THE STARTING MODEL FOR LEAST-SQUARES REFINEMENT | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7 Details: 10.5% PEG 6000 10 MM POTASSIUM PHOSPHATE PH 7.0 100 MM POTASSIUM CHLORIDE 3 MM SODIUM DITHIONITE | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 295 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jun 23, 1995 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. obs: 40065 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2→2.15 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 2.77 / Rsym value: 0.199 / % possible all: 88.5 |
Reflection | *PLUS Num. measured all: 262565 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ISOMORPHOUS WITH DEOXYHEMOGLOBIN A Starting model: DEOXYHEMOGLOBIN A IN THE SAME CELL, UNPUBLISHED RESULTS N.-L. CHAN AND A. ARNONE Resolution: 2→8 Å / σ(F): 2 Details: THE STARTING MODEL FOR REFINEMENT WAS AN UNPUBLISHED DEOXYHEMOGLOBIN A STRUCTURE IN THE SAME CELL.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.167 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |