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Yorodumi- PDB-1j3y: Direct observation of photolysis-induced tertiary structural chan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j3y | ||||||
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Title | Direct observation of photolysis-induced tertiary structural changes in human hemoglobin; Crystal structure of alpha(Fe)-beta(Ni) hemoglobin (laser photolysed) | ||||||
Components |
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Keywords | OXYGEN STORAGE/TRANSPORT / Tertiary structure changes / Crystal photolysis / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
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: 1.55 Å | ||||||
Authors | Adachi, S. / Park, S.-Y. / Tame, J.R.H. / Shiro, Y. / Shibayama, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: Direct observation of photolysis-induced tertiary structural changes in hemoglobin Authors: Adachi, S. / Park, S.-Y. / Tame, J.R.H. / Shiro, Y. / Shibayama, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j3y.cif.gz | 290.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j3y.ent.gz | 230.5 KB | Display | PDB format |
PDBx/mmJSON format | 1j3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j3y_validation.pdf.gz | 999.3 KB | Display | wwPDB validaton report |
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Full document | 1j3y_full_validation.pdf.gz | 1020.8 KB | Display | |
Data in XML | 1j3y_validation.xml.gz | 25.8 KB | Display | |
Data in CIF | 1j3y_validation.cif.gz | 50.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/1j3y ftp://data.pdbj.org/pub/pdb/validation_reports/j3/1j3y | HTTPS FTP |
-Related structure data
Related structure data | 1j3zC 1j40C 1j41C C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein , 2 types, 8 molecules ACEGBDFH
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P69905 #2: Protein | Mass: 15890.198 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871 |
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-Non-polymers , 5 types, 2286 molecules
#3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-CMO / #5: Chemical | ChemComp-HNI / #6: Chemical | #7: 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: 2.39 Å3/Da / Density % sol: 48.6 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / pH: 6.6 Details: PEG 4000, 50mM citrate-ammonium buffer, SMALL TUBES, temperature 293K, pH 6.60 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.6 / Method: unknown | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 25 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 20, 2002 / Details: MONOCHROMATOR |
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: 1.55→20 Å / Num. obs: 153793 / % possible obs: 90.7 % / Observed criterion σ(I): 5.8 / Redundancy: 3.9 % / Rmerge(I) obs: 0.06 |
Reflection shell | Resolution: 1.55→1.61 Å / Rmerge(I) obs: 0.276 / % possible all: 51.8 |
Reflection | *PLUS Lowest resolution: 20 Å / Redundancy: 3.9 % / Num. measured all: 600432 / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS % possible obs: 51.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→19.61 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.895 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.165 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→19.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.213 / Rfactor Rwork: 0.184 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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