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Yorodumi- PDB-1lxc: Crystal Structure of E. Coli Enoyl Reductase-NAD+ with a Bound Ac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lxc | ||||||
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Title | Crystal Structure of E. Coli Enoyl Reductase-NAD+ with a Bound Acrylamide Inhibitor | ||||||
Components | ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH] | ||||||
Keywords | OXIDOREDUCTASE / FABI / ENOYL REDUCTASE | ||||||
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) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / lipid biosynthetic process / 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) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / lipid biosynthetic process / catalytic complex / protein homotetramerization / response to antibiotic / protein-containing complex / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Miller, W.H. / Seefeld, M.A. / Newlander, K.A. / Uzinskas, I.N. / Burgess, W.J. / Heerding, D.A. / Yuan, C.C.K. / Head, M.S. / Payne, D.J. / Rittenhouse, S.F. ...Miller, W.H. / Seefeld, M.A. / Newlander, K.A. / Uzinskas, I.N. / Burgess, W.J. / Heerding, D.A. / Yuan, C.C.K. / Head, M.S. / Payne, D.J. / Rittenhouse, S.F. / Moore, T.D. / Pearson, S.C. / Dewolf, V. / Berry, W.E. / Keller, P.M. / Polizzi, B.J. / Qiu, X. / Janson, C.A. / Huffman, W.F. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2002 Title: Discovery of aminopyridine-based inhibitors of bacterial enoyl-ACP reductase (FabI). Authors: Miller, W.H. / Seefeld, M.A. / Newlander, K.A. / Uzinskas, I.N. / Burgess, W.J. / Heerding, D.A. / Yuan, C.C. / Head, M.S. / Payne, D.J. / Rittenhouse, S.F. / Moore, T.D. / Pearson, S.C. / ...Authors: Miller, W.H. / Seefeld, M.A. / Newlander, K.A. / Uzinskas, I.N. / Burgess, W.J. / Heerding, D.A. / Yuan, C.C. / Head, M.S. / Payne, D.J. / Rittenhouse, S.F. / Moore, T.D. / Pearson, S.C. / Berry, V. / DeWolf Jr., W.E. / Keller, P.M. / Polizzi, B.J. / Qiu, X. / Janson, C.A. / Huffman, W.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lxc.cif.gz | 114.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lxc.ent.gz | 88.8 KB | Display | PDB format |
PDBx/mmJSON format | 1lxc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lx/1lxc ftp://data.pdbj.org/pub/pdb/validation_reports/lx/1lxc | HTTPS FTP |
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-Related structure data
Related structure data | 1lx6C 1c14S S: Starting model for refinement C: citing same article (ref.) |
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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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Details | THE ASYMMETRIC UNIT CAONTAINS A DIMER OF THE TERNARY COMPLEX |
-Components
#1: Protein | Mass: 27892.926 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) References: UniProt: P29132, UniProt: P0AEK4*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH) #2: Chemical | #3: Chemical | #4: 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: 2.67 Å3/Da / Density % sol: 53.96 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES, 2M(NH4)2SO4,5% PEG400, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Qiu, X., (1999) Protein Sci., 8, 2529. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 Å |
Detector | Type: BRANDEIS / Detector: CCD / Date: Nov 22, 1999 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. all: 25117 / Num. obs: 20621 / % possible obs: 82.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 2.4→2.44 Å / Rmerge(I) obs: 0.098 / Mean I/σ(I) obs: 6.9 / % possible all: 43.2 |
Reflection | *PLUS Num. measured all: 91795 / Rmerge(I) obs: 0.053 |
Reflection shell | *PLUS % possible obs: 43.2 % / Rmerge(I) obs: 0.098 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1C14 Resolution: 2.4→20 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 26.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.44 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å / σ(I): 0 / Rfactor Rfree: 0.253 / Rfactor Rwork: 0.199 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.2555 / Rfactor Rwork: 0.215 |