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- PDB-1lxc: Crystal Structure of E. Coli Enoyl Reductase-NAD+ with a Bound Ac... -

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Basic information

Entry
Database: PDB / ID: 1lxc
TitleCrystal Structure of E. Coli Enoyl Reductase-NAD+ with a Bound Acrylamide Inhibitor
ComponentsENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
KeywordsOXIDOREDUCTASE / FABI / ENOYL REDUCTASE
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase [NAD(P)H] activity / 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 [NAD(P)H] activity / 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
Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-AYM / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH] FabI / Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMiller, 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.
CitationJournal: 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
DepositionJun 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
B: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7536
Polymers55,7862
Non-polymers1,9684
Water5,405300
1
A: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
B: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
hetero molecules

A: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
B: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,50712
Polymers111,5724
Non-polymers3,9358
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area22590 Å2
ΔGint-132 kcal/mol
Surface area29780 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)79.580, 79.580, 326.170
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsTHE ASYMMETRIC UNIT CAONTAINS A DIMER OF THE TERNARY COMPLEX

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Components

#1: Protein ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH] / NADH-DEPENDENT ENOYL-ACP REDUCTASE


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 ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-AYM / 3-(6-AMINOPYRIDIN-3-YL)-N-METHYL-N-[(1-METHYL-1H-INDOL-2-YL)METHYL]ACRYLAMIDE


Mass: 320.388 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H20N4O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.96 %
Crystal growTemperature: 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
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
20.1 MHEPES1reservoirpH7.5
32 Mammonium sulfate1reservoir
45 %PEG4001reservoir
520 %ammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 Å
DetectorType: BRANDEIS / Detector: CCD / Date: Nov 22, 1999
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameClassification
CNXrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C14

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
RfactorNum. reflection% reflectionSelection details
Rfree0.253 909 4.8 %RANDOM
Rwork0.199 ---
all-25014 --
obs-20569 82.3 %-
Displacement parametersBiso mean: 26.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.6 Å20.58 Å20 Å2
2--3.6 Å20 Å2
3----7.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3729 0 136 300 4165
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.009
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg1.3
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d21.4
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d0.74
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
LS refinement shellResolution: 2.4→2.44 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2555 24 5 %
Rwork0.215 1680 -
obs-470 46.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2805.PARamWATER.TOP
X-RAY DIFFRACTION3NAD.PARam
X-RAY DIFFRACTION4WATER.PARAM
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
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.007
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_deg21.4
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_deg0.74
LS refinement shell
*PLUS
Rfactor Rfree: 0.2555 / Rfactor Rwork: 0.215

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