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Yorodumi- PDB-4n7n: Capturing the haemoglobin allosteric transition in a single cryst... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4n7n | ||||||
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Title | Capturing the haemoglobin allosteric transition in a single crystal form; Crystal structure of full-liganded human haemoglobin with phosphate at 2.75 A resolution. | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / haemoglobin / allosteric pathway | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.754 Å | ||||||
Authors | Sugiyama, K. / Shibayama, N. / Park, S.Y. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2014 Title: Capturing the hemoglobin allosteric transition in a single crystal form Authors: Shibayama, N. / Sugiyama, K. / Tame, J.R. / Park, S.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n7n.cif.gz | 338.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n7n.ent.gz | 280.8 KB | Display | PDB format |
PDBx/mmJSON format | 4n7n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n7/4n7n ftp://data.pdbj.org/pub/pdb/validation_reports/n7/4n7n | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 6 / Fragment: UNP residues 2-142 / 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.: 6 / Fragment: UNP residues 2-147 / Source method: isolated from a natural source / Details: blood / Source: (natural) Homo sapiens (human) / References: UniProt: P68871 #3: Chemical | ChemComp-HEM / |
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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: 2.37 Å3/Da / Density % sol: 48.04 % |
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Crystal grow | Temperature: 298 K / Method: microbatch under paraffin oil / pH: 6.8 Details: 18% PEG3350, 5% glycerol , pH 6.8, microbatch under paraffin oil, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 17, 2010 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→50 Å / Num. all: 45029 / Num. obs: 45029 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.75→2.8 Å / Rmerge(I) obs: 0.431 / % possible all: 81 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.754→20 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 57.7549 Å2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 143.64 Å2 / Biso mean: 90.4409 Å2 / Biso min: 34.63 Å2
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Refinement step | Cycle: LAST / Resolution: 2.754→20 Å
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Refine LS restraints |
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Xplor file |
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