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Yorodumi- PDB-6bwp: Crystal structure of Deoxy Hemoglobin in complex with beta Cys93 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bwp | ||||||||||||
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Title | Crystal structure of Deoxy Hemoglobin in complex with beta Cys93 modifying agent, TD3 | ||||||||||||
Components |
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Keywords | OXYGEN TRANSPORT / Hemoglobin / Antisickling / Allosteric effector / TD3 | ||||||||||||
Function / homology | Function and homology information nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin 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 / platelet aggregation / hydrogen peroxide catabolic process / oxygen carrier activity / Late endosomal microautophagy / carbon dioxide transport / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / response to hydrogen peroxide / Cytoprotection by HMOX1 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||||||||
Authors | Musayev, F.N. / Safo, R.M. / Safo, M.K. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Mol. Pharm. / Year: 2018 Title: A Triazole Disulfide Compound Increases the Affinity of Hemoglobin for Oxygen and Reduces the Sickling of Human Sickle Cells. Authors: Nakagawa, A. / Ferrari, M. / Schleifer, G. / Cooper, M.K. / Liu, C. / Yu, B. / Berra, L. / Klings, E.S. / Safo, R.S. / Chen, Q. / Musayev, F.N. / Safo, M.K. / Abdulmalik, O. / Bloch, D.B. / Zapol, W.M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bwp.cif.gz | 146.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bwp.ent.gz | 113.3 KB | Display | PDB format |
PDBx/mmJSON format | 6bwp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bwp_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 6bwp_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 6bwp_validation.xml.gz | 34.1 KB | Display | |
Data in CIF | 6bwp_validation.cif.gz | 50.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/6bwp ftp://data.pdbj.org/pub/pdb/validation_reports/bw/6bwp | HTTPS FTP |
-Related structure data
Related structure data | 6bwuC 2dn2S 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
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P69905 #2: Protein | Mass: 15890.198 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871 #3: Chemical | ChemComp-HEM / #4: Chemical | #5: Water | ChemComp-HOH / | Has protein modification | Y | |
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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: 2.19 Å3/Da / Density % sol: 43.94 % |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 6.6 / Details: 3.4M Na Phosphate/NH4 Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54057 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 3, 2017 / Details: VariMax-HF Arc Optics |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54057 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→12.797 Å / Num. obs: 57586 / % possible obs: 97.8 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 21.22 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 5.88 / Num. unique obs: 5764 / Rsym value: 0.165 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2dn2 Resolution: 1.7→12.797 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.16
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→12.797 Å
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Refine LS restraints |
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LS refinement shell |
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