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Yorodumi- PDB-3o2y: Structure-function analysis of human L-Prostaglandin D Synthase b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3o2y | ||||||
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Title | Structure-function analysis of human L-Prostaglandin D Synthase bound with fatty acid | ||||||
Components | Prostaglandin-H2 D-isomerase | ||||||
Keywords | ISOMERASE / Lipocalin / prostaglandin synthase | ||||||
Function / homology | Function and homology information prostaglandin-D synthase / prostaglandin-D synthase activity / Transcriptional regulation of testis differentiation / negative regulation of male germ cell proliferation / regulation of circadian sleep/wake cycle, sleep / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / cyclooxygenase pathway / retinoid binding / prostaglandin biosynthetic process / mast cell degranulation ...prostaglandin-D synthase / prostaglandin-D synthase activity / Transcriptional regulation of testis differentiation / negative regulation of male germ cell proliferation / regulation of circadian sleep/wake cycle, sleep / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / cyclooxygenase pathway / retinoid binding / prostaglandin biosynthetic process / mast cell degranulation / response to glucocorticoid / rough endoplasmic reticulum / fatty acid binding / gene expression / nuclear membrane / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / extracellular space / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Zhou, Y. / Shaw, N. / Li, Y. / Zhao, Y. / Zhang, R. / Liu, Z.-J. | ||||||
Citation | Journal: To be Published Title: Structure-function analysis of human L-Prostaglandin D Synthase bound with fatty acid Authors: Zhou, Y. / Shaw, N. / Li, Y. / Zhao, Y. / Zhang, R. / Liu, Z.-J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o2y.cif.gz | 138.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o2y.ent.gz | 115.8 KB | Display | PDB format |
PDBx/mmJSON format | 3o2y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3o2y_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 3o2y_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3o2y_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | 3o2y_validation.cif.gz | 25.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o2/3o2y ftp://data.pdbj.org/pub/pdb/validation_reports/o2/3o2y | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18089.277 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 29-190 / Mutation: C65A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P41222, prostaglandin-D synthase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: 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 Å3/Da / Density % sol: 38.63 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.8 Details: 0.1M citric acid, pH 3.8, 1.7M ammonium sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2009 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 29672 / Num. obs: 28122 / % possible obs: 92.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.7→1.73 Å / % possible all: 63 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.908 / SU B: 5.849 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.554 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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