[English] 日本語
Yorodumi- PDB-1nej: Crystalline Human Carbonmonoxy Hemoglobin S (Liganded Sickle Cell... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nej | ||||||
---|---|---|---|---|---|---|---|
Title | Crystalline Human Carbonmonoxy Hemoglobin S (Liganded Sickle Cell Hemoglobin) Exhibits The R2 Quaternary State At Neutral pH In The Presence Of Polyethylene Glycol: The 2.1 Angstrom Resolution Crystal Structure | ||||||
Components |
| ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / Mutant human hemoglobin S[betaE6V] / R2 quaternary state / human hemoglobin / 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 / carbon dioxide transport / response to hydrogen peroxide / 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Patskovska, L.N. / Patskovsky, Y.V. / Almo, S.C. / Hirsch, R.E. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: COHbC and COHbS crystallize in the R2 quaternary state at neutral pH in the presence of PEG 4000. Authors: Patskovska, L.N. / Patskovsky, Y.V. / Almo, S.C. / Hirsch, R.E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1nej.cif.gz | 132.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1nej.ent.gz | 104 KB | Display | PDB format |
PDBx/mmJSON format | 1nej.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ne/1nej ftp://data.pdbj.org/pub/pdb/validation_reports/ne/1nej | HTTPS FTP |
---|
-Related structure data
Related structure data | 1m9pSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
| ||||||||||
Details | The biological assembly is a tetramer in the asymmetric unit. |
-Components
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 2 / Fragment: alpha chain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: erythrocytes / Organ: blood / References: UniProt: P69905 #2: Protein | Mass: 15860.216 Da / Num. of mol.: 2 / Fragment: beta chain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: erythrocytes / Organ: blood / References: UniProt: P68871 #3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-CMO / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: 25% PEG 4000, 0.15M HEPES-Na,chloride anion traces; pH 7.1, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 3, 2001 |
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: 2.1→30 Å / Num. all: 32084 / Num. obs: 32084 / % possible obs: 91.7 % / Observed criterion σ(I): 0 / Redundancy: 17 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.67 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 1.6 / Num. unique all: 2240 / % possible all: 64.7 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1M9P Resolution: 2.1→8 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000 / Data cutoff low absF: 0.1 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
|