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- PDB-1d8a: E. COLI ENOYL REDUCTASE/NAD+/TRICLOSAN COMPLEX -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1d8a
TitleE. COLI ENOYL REDUCTASE/NAD+/TRICLOSAN COMPLEX
ComponentsENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
KeywordsOXIDOREDUCTASE / E. COLI ENOYL REDUCTASE / TRICLOSAN
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
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 / Resolution: 2.2 Å
AuthorsLevy, C.W. / Roujeinikova, A. / Sedelnikova, S. / Baker, P.J. / Stuitje, A.R. / Slabas, A.R. / Rice, D.W. / Rafferty, J.B.
Citation
#1: Journal: To be Published
Title: Crystallographic Analysis of Triclosan Bound to Enoyl Reductase
Authors: Roujeinikova, A. / Levy, C.W. / Rowsell, S. / Sedelnikova, S. / Baker, P.J. / Minshull, C.A. / Mistry, A. / Colls, J.G. / Camble, R. / Stuitje, A.R. / Slabas, A.R. / Rafferty, J.B. / ...Authors: Roujeinikova, A. / Levy, C.W. / Rowsell, S. / Sedelnikova, S. / Baker, P.J. / Minshull, C.A. / Mistry, A. / Colls, J.G. / Camble, R. / Stuitje, A.R. / Slabas, A.R. / Rafferty, J.B. / Pauptit, R.A. / Viner, R. / Rice, D.W.
History
DepositionOct 21, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: 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
B: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4296
Polymers55,5232
Non-polymers1,9064
Water2,144119
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A: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
B: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)114,85912
Polymers111,0474
Non-polymers3,8128
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+11/61
Buried area22380 Å2
ΔGint-207 kcal/mol
Surface area29920 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)80.6, 80.6, 327.6
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number178
Space group name H-MP6122

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Components

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


Mass: 27761.730 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-TCL / TRICLOSAN


Mass: 289.542 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H7Cl3O2 / Comment: antifungal, antibiotic, detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 7.5
Details: PEG 400, NA HEPES, AMMONIUM SULPHATE, pH 7.5, VAPOUR DIFFUSION, temperature 290K
Crystal grow
*PLUS
Method: unknown
Details: This particular structure is not described in this paper.

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 25, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.2→999 Å / Num. obs: 153843 / % possible obs: 78 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.057
Reflection shellResolution: 2.18→2.24 Å

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Processing

Software
NameClassification
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
TNTphasing
RefinementResolution: 2.2→20 Å / Stereochemistry target values: ENGH & HUBER /
RfactorSelection details
Rfree0.294 RANDOM
all0.223 -
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3804 0 122 119 4045
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Rfactor all: 0.223
Solvent computation
*PLUS
Displacement parameters
*PLUS

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