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- PDB-4imo: Crystal structure of wild type human Lipocalin PGDS in complex wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4imo | ||||||
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Title | Crystal structure of wild type human Lipocalin PGDS in complex with substrate analog U44069 | ||||||
![]() | Lipocalin-type prostaglandin-D synthase | ||||||
![]() | ISOMERASE / Beta barrel / Endoplasmic reticulum | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lim, S.M. / Chen, D. / Teo, H. / Roos, A. / Nyman, T. / Tresaugues, L. / Pervushin, K. / Nordlund, P. | ||||||
![]() | ![]() Title: Structural and dynamic insights into substrate binding and catalysis of human lipocalin prostaglandin D synthase. Authors: Lim, S.M. / Chen, D. / Teo, H. / Roos, A. / Jansson, A.E. / Nyman, T. / Tresaugues, L. / Pervushin, K. / Nordlund, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 48.6 KB | Display | ![]() |
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PDB format | ![]() | 33.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2wwpC ![]() 4imnC ![]() 2cztS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19748.145 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.79 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M potassium thiocyanate, 30% PEG MME 2000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 198 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 30, 2011 |
Radiation | Monochromator: LN2-cooled, fixed-exit double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97622 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→36.49 Å / Num. all: 12735 / Num. obs: 12735 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 1.88→1.98 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1826 / Rsym value: 0.274 / % possible all: 100 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 2CZT Resolution: 1.88→36.49 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.34 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.165 / ESU R Free: 0.156 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.509 Å2
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Refinement step | Cycle: LAST / Resolution: 1.88→36.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.88→1.929 Å / Total num. of bins used: 20
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