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Yorodumi- PDB-1qg6: CRYSTAL STRUCTURE OF E. COLI ENOYL ACYL CARRIER PROTEIN REDUCTASE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qg6 | ||||||
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Title | CRYSTAL STRUCTURE OF E. COLI ENOYL ACYL CARRIER PROTEIN REDUCTASE IN COMPLEX WITH NAD AND TRICLOSAN | ||||||
Components | PROTEIN (ENOYL-[ACYL-CARRIER PROTEIN] REDUCTASE) | ||||||
Keywords | OXIDOREDUCTASE / FATTY ACID SYNTHESIS / ANTIBACTERIAL | ||||||
Function / homology | Function and homology information enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / NADH binding / biotin biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / lipid biosynthetic process / enoyl-[acyl-carrier-protein] reductase (NADH) activity / catalytic complex / protein homotetramerization / response to antibiotic ...enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / NADH binding / biotin biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / lipid biosynthetic process / enoyl-[acyl-carrier-protein] reductase (NADH) activity / catalytic complex / protein homotetramerization / response to antibiotic / protein-containing complex / membrane / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Rowsell, S. / Pauptit, R.A. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Kinetic and structural characteristics of the inhibition of enoyl (acyl carrier protein) reductase by triclosan. Authors: Ward, W.H. / Holdgate, G.A. / Rowsell, S. / McLean, E.G. / Pauptit, R.A. / Clayton, E. / Nichols, W.W. / Colls, J.G. / Minshull, C.A. / Jude, D.A. / Mistry, A. / Timms, D. / Camble, R. / ...Authors: Ward, W.H. / Holdgate, G.A. / Rowsell, S. / McLean, E.G. / Pauptit, R.A. / Clayton, E. / Nichols, W.W. / Colls, J.G. / Minshull, C.A. / Jude, D.A. / Mistry, A. / Timms, D. / Camble, R. / Hales, N.J. / Britton, C.J. / Taylor, I.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qg6.cif.gz | 209.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qg6.ent.gz | 167.9 KB | Display | PDB format |
PDBx/mmJSON format | 1qg6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qg/1qg6 ftp://data.pdbj.org/pub/pdb/validation_reports/qg/1qg6 | HTTPS FTP |
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-Related structure data
Related structure data | 1dfhS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27761.730 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: FABI / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: P29132, UniProt: P0AEK4*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH) #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-TCL / #4: Water | ChemComp-HOH / | Compound details | ASN A 155 AND ASN A 157 ARE THE RESIDUES EITHER SIDE OF THE CATALYTIC TYROSINE AND HAVE DIHEDRAL ...ASN A 155 AND ASN A 157 ARE THE RESIDUES EITHER SIDE OF THE CATALYTIC TYROSINE AND HAVE DIHEDRAL ANGLES WHICH LIE OUTSIDE THEIR EXPECTED RANGE. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 35 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 5 Details: HANGING DROPS WERE FORMED BY MIXING 4MICROLITRES OF COMPLEX SOLUTION (15MG/ML PROTEIN, 3MM NADH, 0.6MM TRICLOSAN) WITH 4 MICROLITRES OF A RESERVOIR SOLUTION CONTAINING 12-16% (W/V) PEG 400 ...Details: HANGING DROPS WERE FORMED BY MIXING 4MICROLITRES OF COMPLEX SOLUTION (15MG/ML PROTEIN, 3MM NADH, 0.6MM TRICLOSAN) WITH 4 MICROLITRES OF A RESERVOIR SOLUTION CONTAINING 12-16% (W/V) PEG 400 AND 0.1M SODIUM ACETATE PH 4.8-5.2 AT ROOM TEMPERATURE, pH 5.0 | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / PH range low: 5.2 / PH range high: 4.8 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC / Detector: CCD / Date: Sep 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→53.45 Å / Num. obs: 57294 / % possible obs: 78 % / Redundancy: 1.6 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 4.2 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 1.2 / Rsym value: 0.406 / % possible all: 41 |
Reflection | *PLUS % possible obs: 78.2 % / Num. measured all: 92854 |
Reflection shell | *PLUS % possible obs: 40.6 % / Num. unique obs: 4320 / Num. measured obs: 5607 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DFH Resolution: 1.9→100 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 26.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→100 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 98.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 100 Å / σ(F): 0 / % reflection Rfree: 3 % / Rfactor obs: 0.201 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 26.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.279 / % reflection Rfree: 3.1 % / Rfactor Rwork: 0.266 / Rfactor obs: 0.265 |