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Yorodumi- PDB-2w72: DEOXYGENATED STRUCTURE OF A DISTAL SITE HEMOGLOBIN MUTANT PLUS XE -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w72 | ||||||
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Title | DEOXYGENATED STRUCTURE OF A DISTAL SITE HEMOGLOBIN MUTANT PLUS XE | ||||||
Components | (HUMAN HEMOGLOBIN ...) x 3 | ||||||
Keywords | OXYGEN TRANSPORT / IRON / HEME / GLYCATION / TRANSPORT / ACETYLATION / PHOSPHOPROTEIN / PACKING DEFECTS / DISEASE MUTATION / DISTAL SITE POINT MUTATION / HYDROPHOBIC CAVITIES / POLYMORPHISM / GLYCOPROTEIN / METAL-BINDING | ||||||
Function / homology | Function and homology information nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / 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 / oxygen binding / regulation of blood pressure / platelet aggregation / Chaperone Mediated Autophagy / peroxidase activity / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 Å | ||||||
Authors | Miele, A.E. / Draghi, F. / Sciara, G. / Johnson, K.A. / Renzi, F. / Vallone, B. / Brunori, M. / Savino, C. | ||||||
Citation | Journal: Biopolymers / Year: 2009 Title: Pattern of Cavities in Globins: The Case of Human Hemoglobin. Authors: Savino, C. / Miele, A.E. / Draghi, F. / Johnson, K.A. / Sciara, G. / Brunori, M. / Vallone, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w72.cif.gz | 311.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w72.ent.gz | 258 KB | Display | PDB format |
PDBx/mmJSON format | 2w72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w72_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 2w72_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 2w72_validation.xml.gz | 40.7 KB | Display | |
Data in CIF | 2w72_validation.cif.gz | 58.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/2w72 ftp://data.pdbj.org/pub/pdb/validation_reports/w7/2w72 | HTTPS FTP |
-Related structure data
Related structure data | 2w6vC 2w6wC 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
-HUMAN HEMOGLOBIN ... , 3 types, 4 molecules ABDC
#1: Protein | Mass: 15190.353 Da / Num. of mol.: 1 / Fragment: CHAIN ALPHA, RESIDUES 2-142 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: BLOOD / Cell: RED BLOOD CELL / Plasmid: PKK223-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TB-1 / References: UniProt: P69905 | ||
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#2: Protein | Mass: 15962.263 Da / Num. of mol.: 2 / Fragment: CHAIN BETA, RESIDUES 2-147 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: BLOOD / Cell: RED BLOOD CELL / Plasmid: PKK223-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TB-1 / References: UniProt: P68871 #3: Protein | | Mass: 15222.417 Da / Num. of mol.: 1 / Fragment: CHAIN ALPHA, RESIDUES 2-142 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: BLOOD / Cell: RED BLOOD CELL / Plasmid: PKK223-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TB-1 / References: UniProt: P69905 |
-Non-polymers , 6 types, 845 molecules
#4: Chemical | ChemComp-HEM / #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-XE / #7: Chemical | #8: Chemical | ChemComp-PO4 / | #9: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, LEU 30 TO TYR ENGINEERED RESIDUE IN CHAIN A, HIS 59 TO GLN ...ENGINEERED |
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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: 2.4 Å3/Da / Density % sol: 32.5 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 3.2M AMMONIUM SULPHATE 0.1M AMMONIUM PHOSPHATE 0.3M K PHOSPHATE PH 6.7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.8453 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 9, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8453 Å / Relative weight: 1 |
Reflection | Resolution: 1.07→17.6 Å / Num. obs: 250223 / % possible obs: 91.1 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 8.54 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 25.8 |
Reflection shell | Resolution: 1.07→1.12 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 2.5 / % possible all: 90.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QI8 Resolution: 1.07→17.32 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.802 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.82 Å2
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Refinement step | Cycle: LAST / Resolution: 1.07→17.32 Å
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