+Open data
-Basic information
Entry | Database: PDB / ID: 7dy3 | ||||||
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Title | High resolution crystal structure of hemoglobin M Iwate. | ||||||
Components |
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Keywords | OXYGEN TRANSPORT / Hemoglobin / Abnormal Hemoglobin / Allosteric proteins / Oxygen binding | ||||||
Function / homology | Function and homology information nitric oxide transport / cellular oxidant detoxification / hemoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / cellular oxidant detoxification / hemoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid 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 / regulation of blood pressure / Late endosomal microautophagy / Heme signaling / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / response to hydrogen peroxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / platelet aggregation / oxygen binding / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / Factors involved in megakaryocyte development and platelet production / tertiary granule lumen / 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: 1.4 Å | ||||||
Authors | Ohki, M. / Park, S.-Y. | ||||||
Citation | Journal: To Be Published Title: High resolution crystal structure of hemoglobin M Iwate. Authors: Nagatomo, S. / Naoya, S. / Ohki, M. / Park, S.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dy3.cif.gz | 344.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dy3.ent.gz | 224.4 KB | Display | PDB format |
PDBx/mmJSON format | 7dy3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dy3_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
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Full document | 7dy3_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 7dy3_validation.xml.gz | 66.5 KB | Display | |
Data in CIF | 7dy3_validation.cif.gz | 98.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/7dy3 ftp://data.pdbj.org/pub/pdb/validation_reports/dy/7dy3 | HTTPS FTP |
-Related structure data
Related structure data | 2dn2S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15175.380 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P69905 #2: Protein | Mass: 15890.198 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871 #3: Chemical | ChemComp-HEM / #4: Water | ChemComp-HOH / | Has ligand of interest | 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: 2.43 Å3/Da / Density % sol: 49.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 25%w/v PEG 3350, 0.1M HEPES-NaOH buffer, 0.2M lithium sulfate, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: DECTRIS PILATUS3 X 200K-A / Detector: PIXEL / Date: Jun 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→13.08 Å / Num. obs: 228772 / % possible obs: 98.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 8.64 Å2 / CC1/2: 0.998 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 1.4→1.45 Å / Num. unique obs: 862680 / CC1/2: 0.78 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2dn2 Resolution: 1.4→13.08 Å / SU ML: 0.1251 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.1143 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→13.08 Å
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Refine LS restraints |
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LS refinement shell |
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