+Open data
-Basic information
Entry | Database: PDB / ID: 1yxm | ||||||
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Title | Crystal structure of peroxisomal trans 2-enoyl CoA reductase | ||||||
Components | peroxisomal trans 2-enoyl CoA reductase | ||||||
Keywords | OXIDOREDUCTASE / perioxisomes / fatty acid synthesis / enoyl CoA / short-chain dehydrogenases/reductases / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information trans-2-enoyl-CoA reductase (NADPH) / phytol metabolic process / Alpha-oxidation of phytanate / trans-2-enoyl-CoA reductase (NADPH) activity / fatty acid alpha-oxidation / peroxisomal membrane / Peroxisomal protein import / protein localization / fatty acid biosynthetic process / peroxisome ...trans-2-enoyl-CoA reductase (NADPH) / phytol metabolic process / Alpha-oxidation of phytanate / trans-2-enoyl-CoA reductase (NADPH) activity / fatty acid alpha-oxidation / peroxisomal membrane / Peroxisomal protein import / protein localization / fatty acid biosynthetic process / peroxisome / signaling receptor binding / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Jansson, A. / Ng, S. / Arrowsmith, C. / Sharma, S. / Edwards, A.M. / Von Delft, F. / Sundstrom, M. / Oppermann, U. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of perixomal trans 2-enoyl CoA reductase (PECRA) Authors: Jansson, A. / Ng, S. / Arrowsmith, C. / Sharma, S. / Edwards, A.M. / Von Delft, F. / Sundstrom, M. / Oppermann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yxm.cif.gz | 222.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yxm.ent.gz | 177.3 KB | Display | PDB format |
PDBx/mmJSON format | 1yxm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/1yxm ftp://data.pdbj.org/pub/pdb/validation_reports/yx/1yxm | HTTPS FTP |
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-Related structure data
Related structure data | 1vl8S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Refine code: 5
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-Components
#1: Protein | Mass: 32581.270 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: pecr / Plasmid: hPECR-p11T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9BY49, EC: 1.3.1.8 #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-PO4 / | #4: Chemical | ChemComp-ADE / | #5: Water | ChemComp-HOH / | |
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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: 2.2 Å3/Da / Density % sol: 43.1 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Ammonium sulphate, Sodium chloride, Sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 29, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→47.35 Å / Num. all: 88511 / Num. obs: 88511 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 33 Å2 / Rsym value: 0.046 / Net I/σ(I): 42 |
Reflection shell | Resolution: 1.9→2.06 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.445 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1VL8 Resolution: 1.9→47 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 7.325 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.504 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→47 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.901→1.95 Å / Total num. of bins used: 20
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