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- PDB-1i30: E. Coli Enoyl Reductase +NAD+SB385826 -

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Basic information

Entry
Database: PDB / ID: 1i30
TitleE. Coli Enoyl Reductase +NAD+SB385826
ComponentsENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
KeywordsOXIDOREDUCTASE / enoyl reductase / acp / antibiotic
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
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-826 / 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 / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsSeefeld, M.A. / Miller, W.H. / Payne, D.J. / Janson, C.A. / Qiu, X.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2001
Title: Inhibitors of bacterial enoyl acyl carrier protein reductase (FabI): 2,9-disubstituted 1,2,3,4-tetrahydropyrido[3,4-b]indoles as potential antibacterial agents.
Authors: Seefeld, M.A. / Miller, W.H. / Newlander, K.A. / Burgess, W.J. / Payne, D.J. / Rittenhouse, S.F. / Moore, T.D. / DeWolf, W.E. / Keller, P.M. / Qiu, X. / Janson, C.A. / Vaidya, K. / Fosberry, ...Authors: Seefeld, M.A. / Miller, W.H. / Newlander, K.A. / Burgess, W.J. / Payne, D.J. / Rittenhouse, S.F. / Moore, T.D. / DeWolf, W.E. / Keller, P.M. / Qiu, X. / Janson, C.A. / Vaidya, K. / Fosberry, A.P. / Smyth, M.G. / Jaworski, D.D. / Slater-Radosti, C. / Huffman, W.F.
History
DepositionFeb 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2002Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)57,9106
Polymers55,7862
Non-polymers2,1244
Water6,071337
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)115,81912
Polymers111,5724
Non-polymers4,2488
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area20570 Å2
ΔGint-123 kcal/mol
Surface area29970 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)79.490, 79.490, 325.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-1681-

HOH

21B-1553-

HOH

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Components

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


Mass: 27892.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P29132, UniProt: P0AEK4*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-826 / 1,3,4,9-TETRAHYDRO-2-(HYDROXYBENZOYL)-9-[(4-HYDROXYPHENYL)METHYL]-6-METHOXY-2H-PYRIDO[3,4-B]INDOLE


Mass: 398.454 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H22N2O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.66 Å3/Da / Density % sol: 53.81 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, sitting drop / 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 %ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 23223 / % possible obs: 82 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 19
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6 % / Rmerge(I) obs: 0.073 / % possible all: 60
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
Rmerge(I) obs: 0.073

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.4→6 Å / σ(F): 2 / σ(I): 2
RfactorNum. reflectionSelection details
Rfree0.277 925 5%
Rwork0.209 --
obs-18929 -
Refinement stepCycle: LAST / Resolution: 2.4→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3676 0 108 337 4121
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_bond_d0.011
Refinement
*PLUS
Lowest resolution: 6 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.277 / Rfactor Rwork: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS

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