+Open data
-Basic information
Entry | Database: PDB / ID: 6bb5 | ||||||
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Title | Human Oxy-Hemoglobin | ||||||
Components |
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Keywords | OXYGEN TRANSPORT / Hemoglobin / oxygen / R-state | ||||||
Function / homology | Function and homology information nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin 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 / 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: 2.28 Å | ||||||
Authors | Gumpper, R.H. / Terrell, J.R. / Luo, M. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2018 Title: Hemoglobin crystals immersed in liquid oxygen reveal diffusion channels. Authors: Terrell, J.R. / Gumpper, R.H. / Luo, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bb5.cif.gz | 119.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bb5.ent.gz | 94.1 KB | Display | PDB format |
PDBx/mmJSON format | 6bb5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bb5_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6bb5_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6bb5_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 6bb5_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bb/6bb5 ftp://data.pdbj.org/pub/pdb/validation_reports/bb/6bb5 | HTTPS FTP |
-Related structure data
Related structure data | 5wogC 5wohC 2dn1S 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
#1: Protein | Mass: 14894.027 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: 15791.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871 | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.61 % |
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Crystal grow | Temperature: 277 K / Method: batch mode Details: 1 mL 40 mg/mL hemoglobin + 2.65 M (final concentration) phosphate buffer, topped with 100 uL toluene |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 14, 2016 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→51.748 Å / Num. obs: 13363 / % possible obs: 95.88 % / Redundancy: 27.4 % / Net I/σ(I): 38.6 |
Reflection shell | Highest resolution: 2.28 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2DN1 Resolution: 2.28→51.748 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 21.98
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.01 Å2 / Biso mean: 32.9191 Å2 / Biso min: 12.08 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.28→51.748 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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