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- PDB-2wwp: Crystal structure of the human lipocalin-type prostaglandin D synthase -
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Open data
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Basic information
Entry | Database: PDB / ID: 2wwp | ||||||
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Title | Crystal structure of the human lipocalin-type prostaglandin D synthase | ||||||
![]() | PROSTAGLANDIN-H2 D-ISOMERASE | ||||||
![]() | ISOMERASE / CYTOPLASM / TRANSPORT / ENDOPLASMIC RETICULUM / FATTY ACID BIOSYNTHESIS / GOLGI APPARATUS / BETA-TRACE PROTEIN / LIPID SYNTHESIS | ||||||
Function / homology | ![]() prostaglandin-D synthase / Transcriptional regulation of testis differentiation / prostaglandin-D synthase activity / 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 / Transcriptional regulation of testis differentiation / prostaglandin-D synthase activity / 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 / rough endoplasmic reticulum / response to glucocorticoid / 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 | ![]() ![]() ![]() | ||||||
![]() | Roos, A.K. / Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Roos, A.K. / Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotyenova, T. / Kotzch, A. / Kraulis, P. / Markova, N. / Moche, M. / Nielsen, T.K. / Nyman, T. / Persson, C. / Schuler, H. / Schutz, P. / Siponen, M.I. / Svensson, L. / Thorsell, A.G. / Van Den Berg, S. / Wahlberg, E. / Weigelt, J. / Welin, M. / Wisniewska, M. / Nordlund, P. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() 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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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.4 KB | Display | ![]() |
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PDB format | ![]() | 54.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.6 KB | Display | ![]() |
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Full document | ![]() | 436.6 KB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 18.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4imnC ![]() 4imoC ![]() 2cztS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-1, 0.00028, -0.00328), Vector: |
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Components
#1: Protein | Mass: 19748.145 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 36 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 20% PEG3350, 0.2 M SODIUM THIOCYANATE, pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 23, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2→32.65 Å / Num. obs: 20007 / % possible obs: 98.3 % / Observed criterion σ(I): 2.8 / Redundancy: 3.4 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.8 / % possible all: 89.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2CZT Resolution: 2→32.65 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.909 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 17.62 Å2
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Refinement step | Cycle: LAST / Resolution: 2→32.65 Å
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