+Open data
-Basic information
Entry | Database: PDB / ID: 8fdk | ||||||
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Title | Phenylhydroxylamine in Reaction with Human Hemoglobin | ||||||
Components | (Hemoglobin subunit ...) x 2 | ||||||
Keywords | OXYGEN TRANSPORT / hemoglobin / phenylhydroxylamine / nitrosobenzene / hemichrome | ||||||
Function / homology | Function and homology information nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin 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 / 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 / oxygen binding / regulation of blood pressure / platelet aggregation / Chaperone Mediated Autophagy / peroxidase activity / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | Powell, S.M. / Thomas, L.M. / Richter-Addo, G.B. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Inorg.Biochem. / Year: 2023 Title: Crystal structural investigations of heme protein derivatives resulting from reactions of aryl- and alkylhydroxylamines with human hemoglobin. Authors: Powell, S.M. / Wang, B. / Herrera, V.E. / Prather, K.Y. / Nguyen, N.T. / Abucayon, E.G. / Thomas, L.M. / 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 | 8fdk.cif.gz | 157.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fdk.ent.gz | 101 KB | Display | PDB format |
PDBx/mmJSON format | 8fdk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fdk_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 8fdk_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 8fdk_validation.xml.gz | 26.6 KB | Display | |
Data in CIF | 8fdk_validation.cif.gz | 35.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/8fdk ftp://data.pdbj.org/pub/pdb/validation_reports/fd/8fdk | HTTPS FTP |
-Related structure data
Related structure data | 8fdjC 8fdlC 8fdmC 8fdnC 3p5qS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Hemoglobin subunit ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 2 / Fragment: Shr_HID2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P69905 #2: Protein | Mass: 15922.198 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871 |
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-Non-polymers , 4 types, 203 molecules
#3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-NBE / #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Details
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: 2.25 Å3/Da / Density % sol: 45.42 % |
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Crystal grow | Temperature: 298 K / Method: batch mode / pH: 6.81 / Details: 3.2 M sodium/potassium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→38.97 Å / Num. obs: 43238 / % possible obs: 100 % / Redundancy: 2 % / Biso Wilson estimate: 31.35 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 1.89→1.92 Å / Rmerge(I) obs: 0.275 / Num. unique obs: 4130 / CC1/2: 0.896 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3P5Q Resolution: 1.89→32.58 Å / SU ML: 0.2653 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 30.8061 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: 36.34 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89→32.58 Å
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Refine LS restraints |
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LS refinement shell |
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