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Yorodumi- PDB-3hxn: The structure of human carbonmonoxyhemoglobin complex to IHP at 2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hxn | ||||||
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Title | The structure of human carbonmonoxyhemoglobin complex to IHP at 2.0 angstrons resolution. | ||||||
Components | (Hemoglobin subunit ...) x 2 | ||||||
Keywords | OXYGEN TRANSPORT / HEMOGLOBIN / INOSITOL HEXAPHOSPHATE / CARBON MONOXIDE. / Disease mutation / Glycation / Glycoprotein / Heme / Iron / Metal-binding / Phosphoprotein / Transport / Hypotensive agent / Pyruvate / S-nitrosylation / Vasoactive | ||||||
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 / regulation of blood pressure / oxygen binding / 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 Å | ||||||
Authors | Colombo, M.F. / Seixas, F.A.V. | ||||||
Citation | Journal: To be Published Title: The structure of human carbonmonoxyhemoglobin complex to IHP at 2.0 Angstrons resolution Authors: Seixas, F.A.V. / Colombo, M.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hxn.cif.gz | 130.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hxn.ent.gz | 101.8 KB | Display | PDB format |
PDBx/mmJSON format | 3hxn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hxn_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 3hxn_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 3hxn_validation.xml.gz | 29.4 KB | Display | |
Data in CIF | 3hxn_validation.cif.gz | 38.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hx/3hxn ftp://data.pdbj.org/pub/pdb/validation_reports/hx/3hxn | HTTPS FTP |
-Related structure data
Related structure data | 3hhbS 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, 4 molecules ACBD
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: BLOOD / Source: (natural) Homo sapiens (human) / References: UniProt: P69905 #2: Protein | Mass: 15890.198 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, 229 molecules
#3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-CMO / #5: Chemical | ChemComp-IHP / | #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: 2.16 Å3/Da / Density % sol: 43.16 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: CARBONMONOXYHEMOGLOBIN:IHP 1:1, CRYSTALLIZED IN 27% PEG 3350 BUBBLED IN CO- , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 24, 2002 |
Radiation | Monochromator: Si CRYSTAL WITH ASSIMETRIC CUT. 7.25 ASSIMETRIC ANGLE, CONDENSED MODE. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 32661 / Num. obs: 26293 / % possible obs: 92.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.041 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 2→2.06 Å / Num. unique all: 2073 / Rsym value: 0.166 / % possible all: 88.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3HHB - HEMOGLOBIN (DEOXY) Resolution: 2→10 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Details: Average Isotropic B Value for Main Chain Atoms.
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Displacement parameters | Biso mean: 27.783 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati sigma a obs: 0.328 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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