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- PDB-2b35: Crystal structure of Mycobacterium tuberculosis enoyl reductase (... -

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Basic information

Entry
Database: PDB / ID: 2b35
TitleCrystal structure of Mycobacterium tuberculosis enoyl reductase (InhA) inhibited by triclosan
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / enoyl reductase
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / trans-2-enoyl-CoA reductase (NADH) activity / mycolic acid biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NAD+ binding / peptidoglycan-based cell wall / fatty acid binding / fatty acid biosynthetic process ...enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / trans-2-enoyl-CoA reductase (NADH) activity / mycolic acid biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NAD+ binding / peptidoglycan-based cell wall / fatty acid binding / fatty acid biosynthetic process / response to antibiotic / plasma membrane
Similarity search - Function
Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / 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] / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSullivan, T.J. / Truglio, J.J. / Novichenok, P. / Stratton, C. / Zhang, X. / Kaur, T. / Johnson, F. / Boyne, M.S. / Amin, A.
CitationJournal: ACS Chem.Biol. / Year: 2006
Title: High Affinity InhA Inhibitors with Activity against Drug-Resistant Strains of Mycobacterium tuberculosis
Authors: Sullivan, T.J. / Truglio, J.J. / Boyne, M.E. / Novichenok, P. / Zhang, X. / Stratton, C. / Li, H.J. / Kaur, T. / Amin, A. / Johnson, F. / Slayden, R.A. / Kisker, C. / Tonge, P.J.
History
DepositionSep 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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]
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,04618
Polymers171,3296
Non-polymers5,71812
Water0
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)118,03112
Polymers114,2194
Non-polymers3,8128
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
2
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,03112
Polymers114,2194
Non-polymers3,8128
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21630 Å2
ΔGint-206 kcal/mol
Surface area32280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.955, 81.827, 188.656
Angle α, β, γ (deg.)90.00, 95.69, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a tetramer.

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Components

#1: Protein
Enoyl-[acyl-carrier-protein] reductase [NADH] / NADH-dependent enoyl-ACP reductase


Mass: 28554.781 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: inhA / Production host: Escherichia coli (E. coli)
References: UniProt: P0A5Y6, UniProt: P9WGR1*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical
ChemComp-TCL / TRICLOSAN / Triclosan


Mass: 289.542 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H7Cl3O2 / Comment: antifungal, antibiotic, detergent*YM
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM

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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: 44.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: PEG 4000, DMSO, ammonium acetate, NAD+, ADA, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 1, 2002
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→10 Å / Num. all: 63270 / Num. obs: 55089 / % possible obs: 87 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.3→2.37 Å / % possible all: 82.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT1.7data extraction
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→10 Å / Cor.coef. Fo:Fc: 0.856 / Cor.coef. Fo:Fc free: 0.78 / SU B: 11.224 / SU ML: 0.281 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.766 / ESU R Free: 0.376 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.334 2883 5 %RANDOM
Rwork0.268 ---
all0.271 63270 --
obs0.268 57972 87.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.924 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å2-0.33 Å2
2---1.1 Å20 Å2
3---0.84 Å2
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11271 0 366 0 11637
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02211889
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210931
X-RAY DIFFRACTIONr_angle_refined_deg1.4732.00116194
X-RAY DIFFRACTIONr_angle_other_deg0.848325306
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.45751488
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.41223.67455
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.094151867
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5911578
X-RAY DIFFRACTIONr_chiral_restr0.0790.21834
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213100
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022292
X-RAY DIFFRACTIONr_nbd_refined0.1990.22618
X-RAY DIFFRACTIONr_nbd_other0.1910.211085
X-RAY DIFFRACTIONr_nbtor_refined0.1760.25580
X-RAY DIFFRACTIONr_nbtor_other0.0880.26924
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2318
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0690.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.234
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2560.2124
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2260.27
X-RAY DIFFRACTIONr_mcbond_it0.6971.59554
X-RAY DIFFRACTIONr_mcbond_other0.1151.53080
X-RAY DIFFRACTIONr_mcangle_it0.836211855
X-RAY DIFFRACTIONr_scbond_it1.29235179
X-RAY DIFFRACTIONr_scangle_it1.8454.54339
LS refinement shellResolution: 2.3→2.356 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 183 -
Rwork0.275 3635 -
all-3818 -
obs--82.13 %

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