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Yorodumi- PDB-2zb8: Crystal structure of human 15-ketoprostaglandin delta-13-reductas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zb8 | ||||||
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Title | Crystal structure of human 15-ketoprostaglandin delta-13-reductase in complex with NADP and indomethacin | ||||||
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 / : / 15-oxoprostaglandin 13-oxidase [NAD(P)+] 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: 2 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zb8.cif.gz | 93.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zb8.ent.gz | 69.5 KB | Display | PDB format |
PDBx/mmJSON format | 2zb8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zb8_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 2zb8_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2zb8_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 2zb8_validation.cif.gz | 33.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/2zb8 ftp://data.pdbj.org/pub/pdb/validation_reports/zb/2zb8 | HTTPS FTP |
-Related structure data
Related structure data | 2zb3C 2zb4SC 2zb7C C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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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.) 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 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-NAP / | #4: Chemical | ChemComp-IMN / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.84 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: 0.1M MES, pH 5.9, 2.0M ammonium sulfate, 2mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2006 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 26604 / Num. obs: 26205 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 24.7 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2591 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2ZB4 Resolution: 2→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: 46.9 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.005
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