+Open data
-Basic information
Entry | Database: PDB / ID: 1dci | ||||||
---|---|---|---|---|---|---|---|
Title | DIENOYL-COA ISOMERASE | ||||||
Components | DIENOYL-COA ISOMERASE | ||||||
Keywords | LYASE / DIENOYL-COA ISOMERASE | ||||||
Function / homology | Function and homology information delta(3,5)-delta(2,4)-dienoyl-CoA isomerase activity / Peroxisomal protein import / Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / fatty acid beta-oxidation / peroxisome / mitochondrion Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Modis, Y. / Filppula, S.A. / Novikov, D. / Norledge, B. / Hiltunen, J.K. / Wierenga, R.K. | ||||||
Citation | Journal: Structure / Year: 1998 Title: The crystal structure of dienoyl-CoA isomerase at 1.5 A resolution reveals the importance of aspartate and glutamate sidechains for catalysis. Authors: Modis, Y. / Filppula, S.A. / Novikov, D.K. / Norledge, B. / Hiltunen, J.K. / Wierenga, R.K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1dci.cif.gz | 195.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1dci.ent.gz | 155.6 KB | Display | PDB format |
PDBx/mmJSON format | 1dci.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dci_validation.pdf.gz | 403.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1dci_full_validation.pdf.gz | 412.9 KB | Display | |
Data in XML | 1dci_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 1dci_validation.cif.gz | 32.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/1dci ftp://data.pdbj.org/pub/pdb/validation_reports/dc/1dci | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Components on special symmetry positions |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-Components
#1: Protein | Mass: 30416.055 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: WISTAR / Cell line: BL21 / Cellular location: PEROXISOME, MITOCHONDRIA / Organ: LIVER / Organelle: PEROXISOME, MITOCHONDRIA / Plasmid: PET3A (NOVAGEN) / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) LYSS / References: UniProt: Q62651, enoyl-CoA hydratase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-MG / #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: 2.6 Å3/Da / Density % sol: 50 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 8.75 / Details: pH 8.75 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / pH: 7 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9092 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1997 / Details: BENT MIRROR |
Radiation | Monochromator: GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9092 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→25 Å / Num. obs: 153741 / % possible obs: 94.1 % / Observed criterion σ(I): 3 / Redundancy: 4.1 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.7 / % possible all: 84 |
Reflection shell | *PLUS % possible obs: 84.3 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ISOMORPHOUS REPLACEMENT / Resolution: 1.5→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.3 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→15 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.176 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |