+Open data
-Basic information
Entry | Database: PDB / ID: 3d7o | ||||||
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Title | Human hemoglobin, nitrogen dioxide anion modified | ||||||
Components | (Hemoglobin subunit ...) x 2 | ||||||
Keywords | OXYGEN TRANSPORT / Human Hemoglobin / Acetylation / Disease mutation / Glycation / Glycoprotein / Heme / Iron / Metal-binding / Polymorphism / Transport / Hypotensive agent / Pyruvate / S-nitrosylation / Vasoactive | ||||||
Function / homology | Function and homology information cellular oxidant detoxification / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / hemoglobin binding / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...cellular oxidant detoxification / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / hemoglobin binding / 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 / 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 / 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 / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Yi, J. / Safo, M.K. / Richter-Addo, G.B. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: The nitrite anion binds to human hemoglobin via the uncommon O-nitrito mode. Authors: Yi, J. / Safo, M.K. / Richter-Addo, G.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d7o.cif.gz | 75.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d7o.ent.gz | 54.7 KB | Display | PDB format |
PDBx/mmJSON format | 3d7o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/3d7o ftp://data.pdbj.org/pub/pdb/validation_reports/d7/3d7o | HTTPS FTP |
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-Related structure data
Related structure data | 1irdS 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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Unit cell |
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-Components
-Hemoglobin subunit ... , 2 types, 2 molecules AB
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P69905 |
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#2: Protein | Mass: 15890.198 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871 |
-Non-polymers , 4 types, 157 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MBN / | #6: 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: 2.21 Å3/Da / Density % sol: 44.43 % |
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Crystal grow | Temperature: 295 K / Method: liquid diffusion / pH: 6.8 Details: Sodium phosphate, Potassium phosphate, Toluene, Hemoglobin, pH 6.8, LIQUID DIFFUSION, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 16, 2008 / Details: Osmic |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→16.37 Å / Num. all: 26808 / Num. obs: 26808 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.74 % / Biso Wilson estimate: 36.6 Å2 / Rmerge(I) obs: 0.082 / Χ2: 0.96 / Net I/σ(I): 10.2 / Scaling rejects: 1568 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 2.9 / Num. measured all: 10752 / Num. unique all: 2558 / Χ2: 1.16 / % possible all: 98.3 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1IRD Resolution: 1.8→16.37 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.01 / SU ML: 0.094 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.151 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 28.993 Å2
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Refine analyze | Luzzati coordinate error obs: 0.23 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→16.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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