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Yorodumi- PDB-4oru: Three-dimensional structure of the C65A mutant of Human lipocalin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oru | ||||||
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Title | Three-dimensional structure of the C65A mutant of Human lipocalin-type Prostaglandin D Synthase holo-form second space group | ||||||
Components | Prostaglandin-H2 D-isomerase | ||||||
Keywords | ISOMERASE / LIPOCALIN-TYPE PROSTAGLANDIN-D SYNTHASE / PEG | ||||||
Function / homology | Function and homology information prostaglandin-D synthase / prostaglandin-D synthase activity / negative regulation of male germ cell proliferation / Transcriptional regulation of testis differentiation / 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 / negative regulation of male germ cell proliferation / Transcriptional regulation of testis differentiation / 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: 1.55 Å | ||||||
Authors | Perduca, M. / Bovi, M. / Bertinelli, M. / Bertini, E. / Destefanis, L. / Carrizo, M.E. / Capaldi, S. / Monaco, H.L. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: High-resolution structures of mutants of residues that affect access to the ligand-binding cavity of human lipocalin-type prostaglandin D synthase. Authors: Perduca, M. / Bovi, M. / Bertinelli, M. / Bertini, E. / Destefanis, L. / Carrizo, M.E. / Capaldi, S. / Monaco, H.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4oru.cif.gz | 141.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oru.ent.gz | 110.1 KB | Display | PDB format |
PDBx/mmJSON format | 4oru.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4oru_validation.pdf.gz | 630.7 KB | Display | wwPDB validaton report |
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Full document | 4oru_full_validation.pdf.gz | 635.9 KB | Display | |
Data in XML | 4oru_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 4oru_validation.cif.gz | 19.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/4oru ftp://data.pdbj.org/pub/pdb/validation_reports/or/4oru | HTTPS FTP |
-Related structure data
Related structure data | 4orrSC 4orsC 4orwC 4orxC 4oryC 4os0C 4os3C 4os8C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 21017.717 Da / Num. of mol.: 2 / Mutation: C65A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTGDS, PDS / Production host: Escherichia coli (E. coli) / References: UniProt: P41222, prostaglandin-D synthase #2: Chemical | ChemComp-PEU / | #3: Water | ChemComp-HOH / | Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da / Density % sol: 32.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 30% PEG 4000, 0.2M Ammonium Sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 5, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→45.56 Å / Num. all: 44356 / Num. obs: 44187 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.55→1.63 Å / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 3.3 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4ORR Resolution: 1.55→45.565 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 23.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→45.565 Å
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Refine LS restraints |
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LS refinement shell |
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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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