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Yorodumi- PDB-6z5o: CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6z5o | ||||||
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Title | CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-1 (RPMFE1) COMPLEXED WITH COENZYME-A AND OXIDISED NICOTINAMIDE ADENINE DINUCLEOTIDE | ||||||
Components | Peroxisomal bifunctional enzyme | ||||||
Keywords | OXIDOREDUCTASE / COENZYME-A / BETA OXIDATION / PEROXISOME / hydratase / 3S-hydroxyacyl-CoA-dehydrogenase | ||||||
Function / homology | Function and homology information Beta-oxidation of very long chain fatty acids / intramolecular oxidoreductase activity, transposing C=C bonds / Peroxisomal protein import / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / long-chain-3-hydroxyacyl-CoA dehydrogenase activity / 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / 3-hydroxyacyl-CoA dehydrogenase activity / enoyl-CoA hydratase activity ...Beta-oxidation of very long chain fatty acids / intramolecular oxidoreductase activity, transposing C=C bonds / Peroxisomal protein import / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / long-chain-3-hydroxyacyl-CoA dehydrogenase activity / 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / 3-hydroxyacyl-CoA dehydrogenase activity / enoyl-CoA hydratase activity / fatty acid beta-oxidation / NAD+ binding / peroxisome / enzyme binding / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Wierenga, R.K. / Sridhar, S. / Kiema, T.R. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2020 Title: Crystallographic binding studies of rat peroxisomal multifunctional enzyme type 1 with 3-ketodecanoyl-CoA: capturing active and inactive states of its hydratase and dehydrogenase catalytic sites. Authors: Sridhar, S. / Schmitz, W. / Hiltunen, J.K. / Venkatesan, R. / Bergmann, U. / Kiema, T.R. / Wierenga, R.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6z5o.cif.gz | 182.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z5o.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6z5o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z5/6z5o ftp://data.pdbj.org/pub/pdb/validation_reports/z5/6z5o | HTTPS FTP |
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-Related structure data
Related structure data | 6z5fC 6z5vC 5omoS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.23729/062a3142-8cdd-408e-8797-62209794bb0b Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules AAA
#1: Protein | Mass: 80931.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: peroxisomal / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ehhadh / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P07896, enoyl-CoA hydratase, Delta3-Delta2-enoyl-CoA isomerase, 3-hydroxyacyl-CoA dehydrogenase |
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-Non-polymers , 6 types, 676 molecules
#2: Chemical | ChemComp-NAD / | ||||||||
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#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-COA / | #6: Chemical | ChemComp-NCA / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 47.96 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 75mM MES, pH 6; 16%w/v PEG 4000; 125mM ammonium sulfate. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972957 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 31, 2018 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972957 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→48.9 Å / Num. obs: 80675 / % possible obs: 95.1 % / Redundancy: 8.13 % / Biso Wilson estimate: 21.4 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.046 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.7→1.73 Å / Rmerge(I) obs: 1.005 / Mean I/σ(I) obs: 2 / Num. unique obs: 4187 / CC1/2: 0.811 / Rpim(I) all: 0.37 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5OMO Resolution: 1.7→48.9 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.532 / SU ML: 0.082 / Cross valid method: NONE / ESU R: 0.119 / ESU R Free: 0.12 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.328 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→48.9 Å
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Refine LS restraints |
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LS refinement shell |
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