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- PDB-1qsg: CRYSTAL STRUCTURE OF ENOYL REDUCTASE INHIBITION BY TRICLOSAN -

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Basic information

Entry
Database: PDB / ID: 1qsg
TitleCRYSTAL STRUCTURE OF ENOYL REDUCTASE INHIBITION BY TRICLOSAN
ComponentsENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
KeywordsOXIDOREDUCTASE / 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
alpha-D-glucopyranose / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / TRICLOSAN / 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: 1.75 Å
AuthorsStewart, M.J. / Parikh, S. / Xiao, G. / Tonge, P.J. / Kisker, C.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Structural basis and mechanism of enoyl reductase inhibition by triclosan.
Authors: Stewart, M.J. / Parikh, S. / Xiao, G. / Tonge, P.J. / Kisker, C.
History
DepositionJun 21, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
B: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
C: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
D: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
E: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
F: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
G: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
H: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,46732
Polymers225,4028
Non-polymers9,06524
Water24,3201350
1
A: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
B: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
C: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
D: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,23316
Polymers112,7014
Non-polymers4,53212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22690 Å2
ΔGint-201 kcal/mol
Surface area32310 Å2
MethodPISA, PQS
2
E: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
F: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
G: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
H: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,23316
Polymers112,7014
Non-polymers4,53212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22820 Å2
ΔGint-201 kcal/mol
Surface area32010 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)73.733, 82.077, 84.177
Angle α, β, γ (deg.)89.54, 87.43, 77.77
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 28175.201 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET15B / Production host: Escherichia coli (E. coli)
References: UniProt: P29132, UniProt: P0AEK4*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Sugar
ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-TCL / TRICLOSAN


Mass: 289.542 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C12H7Cl3O2 / Comment: antifungal, antibiotic, detergent*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1350 / 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: 2.2 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, AMMONIUM ACETATE, SODIUM ACETATE, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Feb 7, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. obs: 183224 / % possible obs: 94.2 % / Observed criterion σ(I): 0 / Redundancy: 1.85 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 13.2
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 1.64 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 1.6 / % possible all: 90.5
Reflection shell
*PLUS
% possible obs: 90.5 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DFI

1dfi


Resolution: 1.75→20 Å / SU B: 3.26 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.12
RfactorNum. reflection% reflectionSelection details
Rfree0.215 3664 2 %RANDOM
Rwork0.172 ---
obs-182903 94.2 %-
Displacement parametersBiso mean: 27.18 Å2
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15353 0 584 1350 17287
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d0.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.035
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.456
X-RAY DIFFRACTIONp_mcangle_it3.04
X-RAY DIFFRACTIONp_scbond_it3.038
X-RAY DIFFRACTIONp_scangle_it4.308
X-RAY DIFFRACTIONp_plane_restr0.022
X-RAY DIFFRACTIONp_chiral_restr0.109
X-RAY DIFFRACTIONp_singtor_nbd0.166
X-RAY DIFFRACTIONp_multtor_nbd0.258
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.157
X-RAY DIFFRACTIONp_planar_tor4
X-RAY DIFFRACTIONp_staggered_tor13.8
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor27.3
X-RAY DIFFRACTIONp_special_tor

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