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Yorodumi- PDB-3dut: The high salt (phosphate) crystal structure of deoxy hemoglobin E... -
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-Basic information
Entry | Database: PDB / ID: 3dut | ||||||
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Title | The high salt (phosphate) crystal structure of deoxy hemoglobin E (GLU26LYS) at physiological pH (pH 7.35) | ||||||
Components |
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Keywords | OXYGEN BINDING / hemoglobin E oxygen transport beta thalassemia physiological / Disease mutation / Glycation / Glycoprotein / Heme / Iron / Metal-binding / Oxygen transport / Transport / Hypotensive agent / Pyruvate / S-nitrosylation / Vasoactive | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å | ||||||
Authors | Malashkevich, V.N. / Balazs, T.C. / Almo, S.C. / Hirsch, R.E. | ||||||
Citation | Journal: To be Published Title: The high salt (phosphate) crystal structure of deoxy hemoglobin E (GLU26LYS) at physiological pH (pH 7.35) Authors: Malashkevich, V.N. / Balazs, T.C. / Almo, S.C. / Hirsch, R.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dut.cif.gz | 135.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dut.ent.gz | 106.3 KB | Display | PDB format |
PDBx/mmJSON format | 3dut.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/du/3dut ftp://data.pdbj.org/pub/pdb/validation_reports/du/3dut | HTTPS FTP |
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-Related structure data
Related structure data | |
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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
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HBA1, HBA2 / References: UniProt: P69905 #2: Protein | Mass: 15890.265 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HBB / References: UniProt: P68871 #3: Chemical | ChemComp-HEM / #4: Chemical | #5: 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: 2.11 Å3/Da / Density % sol: 41.57 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.35 Details: 1.65 M potassium phosphate, 0.05 M Bis-Tris, pH 7.35, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X3A / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 2, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 4 % / Av σ(I) over netI: 14.6 / Number: 355222 / Rmerge(I) obs: 0.042 / Χ2: 1.09 / D res high: 1.43 Å / D res low: 50 Å / Num. obs: 89125 / % possible obs: 93.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.43→50 Å / Num. obs: 89125 / % possible obs: 93.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.042 / Χ2: 1.085 / Net I/σ(I): 14.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 49.17 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→9.99 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.744 / SU B: 6.014 / SU ML: 0.102 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.12 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 67.22 Å2 / Biso mean: 27.598 Å2 / Biso min: 10.4 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→9.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.589 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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