[English] 日本語
Yorodumi- PDB-2zb4: Crystal structure of human 15-ketoprostaglandin delta-13-reductas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zb4 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human 15-ketoprostaglandin delta-13-reductase in complex with NADP and 15-keto-PGE2 | ||||||
Components | Prostaglandin reductase 2 | ||||||
Keywords | OXIDOREDUCTASE / Rossmann fold / Alternative splicing / Cytoplasm / NADP | ||||||
Function / homology | Function and homology information 13,14-dehydro-15-oxoprostaglandin 13-reductase / 13-prostaglandin reductase activity / 15-oxoprostaglandin 13-oxidase activity / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / prostaglandin metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | ||||||
Authors | Wu, Y.H. / Wang, A.H.J. / Ko, T.P. / Guo, R.T. / Hu, S.M. / Chuang, L.M. | ||||||
Citation | Journal: Structure / Year: 2008 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2zb4.cif.gz | 99.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2zb4.ent.gz | 73.6 KB | Display | PDB format |
PDBx/mmJSON format | 2zb4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/2zb4 ftp://data.pdbj.org/pub/pdb/validation_reports/zb/2zb4 | HTTPS FTP |
---|
-Related structure data
Related structure data | 2zb3SC 2zb7C 2zb8C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 38961.285 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTGR2, ZADH1 / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8N8N7, 13,14-dehydro-15-oxoprostaglandin 13-reductase | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-NAP / | #4: Chemical | ChemComp-5OP / ( | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.4 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
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 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.3 Å2 | |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.63→30 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.63→1.69 Å / Rfactor Rfree error: 0.013
|