[English] 日本語
Yorodumi- PDB-2x7h: Crystal structure of the human MGC45594 gene product in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x7h | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the human MGC45594 gene product in complex with fenoprofen | ||||||
Components | ZINC-BINDING ALCOHOL DEHYDROGENASE DOMAIN-CONTAINING PROTEIN 2 | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information 13,14-dehydro-15-oxoprostaglandin 13-reductase / : / 15-oxoprostaglandin 13-oxidase [NAD(P)+] activity / negative regulation of fat cell differentiation / peroxisome / zinc ion binding Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Shafqat, N. / Yue, W.W. / Ugochukwu, E. / Niesen, F. / Vollmar, M. / Chaikuad, A. / Pike, A.C.W. / von Delft, F. / Smee, C. / Arrowsmith, C. ...Shafqat, N. / Yue, W.W. / Ugochukwu, E. / Niesen, F. / Vollmar, M. / Chaikuad, A. / Pike, A.C.W. / von Delft, F. / Smee, C. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Bountra, C. / Oppermann, U. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Human Mgc45594 Gene Product in Complex with Fenoprofen Authors: Shafqat, N. / Yue, W.W. / Ugochukwu, E. / Niesen, F. / Vollmar, M. / Chaikuad, A. / Pike, A.C.W. / von Delft, F. / Smee, C. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Bountra, C. / Oppermann, U. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2x7h.cif.gz | 277.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2x7h.ent.gz | 224.8 KB | Display | PDB format |
PDBx/mmJSON format | 2x7h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2x7h_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2x7h_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 2x7h_validation.xml.gz | 32.1 KB | Display | |
Data in CIF | 2x7h_validation.cif.gz | 46.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/2x7h ftp://data.pdbj.org/pub/pdb/validation_reports/x7/2x7h | HTTPS FTP |
-Related structure data
Related structure data | 2wekS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||
2 |
| |||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
|
-Components
#1: Protein | Mass: 39475.199 Da / Num. of mol.: 2 / Fragment: DEHYDROGENASE REDUCTASE DOMAIN, RESIDUES 25-371 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)-R3-PRARE2 / References: UniProt: Q8N4Q0, Oxidoreductases #2: Chemical | ChemComp-PFN / #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.21 % / Description: NONE |
---|---|
Crystal grow | Details: 0.5M NA MALONATE PH7.0, 0.25W/V JEFFAMINE ED 2001_PH7.0, 8PH HEPES. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9809 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 17, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9809 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→31.52 Å / Num. obs: 84512 / % possible obs: 92.4 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.9 / % possible all: 90.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WEK Resolution: 1.6→75.46 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.971 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 18.748 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→75.46 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|