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Yorodumi- PDB-1ps9: The Crystal Structure and Reaction Mechanism of E. coli 2,4-Dieno... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ps9 | ||||||
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Title | The Crystal Structure and Reaction Mechanism of E. coli 2,4-Dienoyl CoA Reductase | ||||||
Components | 2,4-dienoyl-CoA reductase | ||||||
Keywords | OXIDOREDUCTASE / IRON-SULFUR / TIM BARREL / FLAVODOXIN / FLAVIN / ELECTRON TRANSFER / HYDRIDE TRANSFER | ||||||
Function / homology | Function and homology information 2,4-dienoyl-CoA reductase [(2E)-enoyl-CoA-producing] / fatty acid beta-oxidation, unsaturated, even number, reductase/isomerase pathway / 2,4-dienoyl-CoA reductase (NADPH) activity / FAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å | ||||||
Authors | Hubbard, P.A. / Liang, X. / Schulz, H. / Kim, J.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: The crystal structure and reaction mechanism of Escherichia coli 2,4-dienoyl-CoA reductase Authors: Hubbard, P.A. / Liang, X. / Schulz, H. / Kim, J.J. #1: Journal: Eur.J.Biochem. / Year: 1997 Title: Cloning and expression of the fadH gene and characterization of the gene product 2,4-dienoyl coenzyme A reductase from Escherichia coli Authors: He, X.-Y. / Yang, S.-Y. / Schulz, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ps9.cif.gz | 157.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ps9.ent.gz | 119 KB | Display | PDB format |
PDBx/mmJSON format | 1ps9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ps/1ps9 ftp://data.pdbj.org/pub/pdb/validation_reports/ps/1ps9 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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 A
#1: Protein | Mass: 72627.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: FADH / Plasmid: pND-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: UniProt: P42593, 2,4-dienoyl-CoA reductase [(2E)-enoyl-CoA-producing] |
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-Non-polymers , 7 types, 381 molecules
#2: Chemical | #3: Chemical | ChemComp-SF4 / | #4: Chemical | ChemComp-FAD / | #5: Chemical | ChemComp-FMN / | #6: Chemical | ChemComp-NAP / | #7: Chemical | ChemComp-MDE / | #8: 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: 2.72 Å3/Da / Density % sol: 54.77 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292.5 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 5000, sodium acetate, ammonium sulfate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 19.5K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.2→30 Å / Num. obs: 74790 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.1 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 30.3 | ||||||||||||||||||
Reflection shell | Resolution: 2.2→2.26 Å / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 7.8 / Num. unique all: 2553 / Rsym value: 0.249 / % possible all: 61.2 | ||||||||||||||||||
Reflection | *PLUS Num. obs: 42467 / Num. measured all: 898148 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 61.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.2→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: 39.5 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å
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Refinement | *PLUS Rfactor Rfree: 0.244 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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