+Open data
-Basic information
Entry | Database: PDB / ID: 4m4a | ||||||
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Title | Human Hemoglobin Nitromethane Modified | ||||||
Components | (Hemoglobin subunit ...) x 2 | ||||||
Keywords | OXYGEN TRANSPORT / R-state / human hemoglobin / nitromethane modified | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Yi, J. / Guan, Y. / Thomas, L.M. / Richter-Addo, G.B. | ||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2013 Title: Degradation of human hemoglobin by organic C-nitroso compounds. Authors: Yi, J. / Ye, G. / Thomas, L.M. / 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 | 4m4a.cif.gz | 74.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m4a.ent.gz | 54.3 KB | Display | PDB format |
PDBx/mmJSON format | 4m4a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/4m4a ftp://data.pdbj.org/pub/pdb/validation_reports/m4/4m4a | HTTPS FTP |
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-Related structure data
Related structure data | 4m4bC 3d7oS C: citing same article (ref.) 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 on special symmetry positions |
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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 / Details: Blood / Source: (natural) Homo sapiens (human) / Strain: 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 / Details: Blood / Source: (natural) Homo sapiens (human) / Strain: Human / References: UniProt: P68871 |
-Non-polymers , 4 types, 151 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #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: 2.22 Å3/Da / Density % sol: 44.53 % |
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Crystal grow | Temperature: 295 K / Method: liquid diffusion / pH: 6.8 Details: sodium phosphate, potassium phosphate, toluene, 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: Jan 22, 2009 / 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: 2.05→21.4 Å / Num. all: 18441 / Num. obs: 18023 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.13 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 6.44 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 4.8 / Num. unique all: 1661 / % possible all: 92.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3D7O Resolution: 2.05→21.4 Å / SU ML: 0.25 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.66 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.881 Å2 / ksol: 0.359 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→21.4 Å
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Refine LS restraints |
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LS refinement shell |
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