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- PDB-2zb4: Crystal structure of human 15-ketoprostaglandin delta-13-reductas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2zb4 | ||||||
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Title | Crystal structure of human 15-ketoprostaglandin delta-13-reductase in complex with NADP and 15-keto-PGE2 | ||||||
![]() | Prostaglandin reductase 2 | ||||||
![]() | OXIDOREDUCTASE / Rossmann fold / Alternative splicing / Cytoplasm / NADP | ||||||
Function / homology | ![]() 13,14-dehydro-15-oxoprostaglandin 13-reductase / 15-oxoprostaglandin 13-oxidase [NAD(P)+] activity / : / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / prostaglandin metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wu, Y.H. / Wang, A.H.J. / Ko, T.P. / Guo, R.T. / Hu, S.M. / Chuang, L.M. | ||||||
![]() | ![]() Title: Structural basis for catalytic and inhibitory mechanisms of human prostaglandin reductase PTGR2. Authors: Wu, Y.H. / Ko, T.P. / Guo, R.T. / Hu, S.M. / Chuang, L.M. / Wang, A.H.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99.8 KB | Display | ![]() |
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PDB format | ![]() | 73.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 970.3 KB | Display | ![]() |
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Full document | ![]() | 992.3 KB | Display | |
Data in XML | ![]() | 24.9 KB | Display | |
Data in CIF | ![]() | 38 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2zb3SC ![]() 2zb7C ![]() 2zb8C 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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Unit cell |
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Components
#1: Protein | Mass: 38961.285 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8N8N7, 13,14-dehydro-15-oxoprostaglandin 13-reductase | ||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-NAP / | #4: Chemical | ChemComp-5OP / ( | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.4 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: 0.1M MES, 2.0M ammonium sulfate, 2mM DTT, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2006 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→30 Å / Num. all: 42773 / Num. obs: 41704 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 29.5 |
Reflection shell | Resolution: 1.63→1.69 Å / Redundancy: 6 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 7.4 / Num. unique all: 4142 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2ZB3 Resolution: 1.63→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 24.3 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.63→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.63→1.69 Å / Rfactor Rfree error: 0.013
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