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Yorodumi- PDB-1k0y: X-ray Crystallographic Analyses of Symmetrical Allosteric Effecto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k0y | ||||||
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Title | X-ray Crystallographic Analyses of Symmetrical Allosteric Effectors of Hemoglobin. Compounds Designed to Link Primary and Secondary Binding Sites | ||||||
Components |
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Keywords | OXYGEN STORAGE/TRANSPORT / hemoglobin / allosteric / T state / deoxy / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin 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 / platelet aggregation / hydrogen peroxide catabolic process / oxygen carrier activity / Late endosomal microautophagy / Heme signaling / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / response to hydrogen peroxide / Cytoprotection by HMOX1 / 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 / 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 / FOURIER SYNTHESIS / Resolution: 1.87 Å | ||||||
Authors | Safo, M.K. / Boyiri, T. / Burnett, J.C. / Danso-Danquah, R. / Moure, C.M. / Joshi, G.S. / Abraham, D.J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: X-ray crystallographic analyses of symmetrical allosteric effectors of hemoglobin: compounds designed to link primary and secondary binding sites. Authors: Safo, M.K. / Boyiri, T. / Burnett, J.C. / Danso-Danquah, R. / Moure, C.M. / Joshi, G.S. / Abraham, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k0y.cif.gz | 133.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k0y.ent.gz | 103.7 KB | Display | PDB format |
PDBx/mmJSON format | 1k0y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k0y_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 1k0y_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 1k0y_validation.xml.gz | 27.3 KB | Display | |
Data in CIF | 1k0y_validation.cif.gz | 37 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/1k0y ftp://data.pdbj.org/pub/pdb/validation_reports/k0/1k0y | HTTPS FTP |
-Related structure data
Related structure data | 1hhb 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
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: blood / 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) / Tissue: blood / References: UniProt: P68871 |
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-Non-polymers , 4 types, 265 molecules
#3: Chemical | ChemComp-HEM / #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: 2.27 Å3/Da / Density % sol: 45.72 % |
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Crystal grow | Temperature: 298 K / Method: liquid diffusion / pH: 6.5 Details: Ammonium sulfate, ammonium phosphate, ferrous citrate, pH 6.5, LIQUID DIFFUSION, temperature 298K |
Crystal grow | *PLUS Method: batch method / Details: Safo, M.K., (2001) Protein Sci, 10, 951. |
Components of the solutions | *PLUS Conc.: 3.6 M / Common name: sulfate/phosphate |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Aug 22, 1997 / Details: mirrors |
Radiation | Monochromator: MSC Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→53 Å / Num. all: 42624 / Num. obs: 42624 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 24.16 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.87→1.94 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.151 / Mean I/σ(I) obs: 4.5 / Num. unique all: 3287 / % possible all: 73.8 |
Reflection | *PLUS Lowest resolution: 53 Å / Num. measured all: 119063 |
Reflection shell | *PLUS % possible obs: 73.8 % / Num. unique obs: 3287 / Num. measured obs: 8433 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1HHB 1hhb Resolution: 1.87→53 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh and Huber Details: Anomalous data used for refinement. Bulk solvent correction used during refinement.
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Displacement parameters | Biso mean: 22 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.87→53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.87→1.96 Å
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 53 Å / σ(F): 0 / Rfactor obs: 0.163 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 22 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.286 / Rfactor Rwork: 0.275 |