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- PDB-4tro: Structure of the enoyl-ACP reductase of Mycobacterium tuberculosi... -

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Basic information

Entry
Database: PDB / ID: 4tro
TitleStructure of the enoyl-ACP reductase of Mycobacterium tuberculosis InhA, inhibited with the active metabolite of isoniazid
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / isoniazid
Function / homology
Function and homology information


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 / 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 / Chem-ZID / 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: 1.4 Å
AuthorsChollet, A. / Julien, S. / Mourey, L. / Maveyraud, L.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Crystal structure of the enoyl-ACP reductase of Mycobacterium tuberculosis (InhA) in the apo-form and in complex with the active metabolite of isoniazid pre-formed by a biomimetic approach.
Authors: Chollet, A. / Mourey, L. / Lherbet, C. / Delbot, A. / Julien, S. / Baltas, M. / Bernadou, J. / Pratviel, G. / Maveyraud, L. / Bernardes-Genisson, V.
History
DepositionJun 17, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,82211
Polymers28,5551
Non-polymers2,26710
Water4,792266
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,28744
Polymers114,2194
Non-polymers9,06840
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
crystal symmetry operation12_545x,x-y-1,-z+1/31
Buried area30900 Å2
ΔGint-170 kcal/mol
Surface area33080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.434, 97.434, 139.752
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-435-

HOH

21A-447-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Enoyl-[acyl-carrier-protein] reductase [NADH]


Mass: 28554.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: inhA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: M9TGV3, UniProt: P9WGR1*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)

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Non-polymers , 6 types, 276 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-ZID / ISONICOTINIC-ACETYL-NICOTINAMIDE-ADENINE DINUCLEOTIDE


Mass: 768.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H30N8O15P2
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 8-10 % (v/v) 2-methyl-2,4-pentanediol, 0.1 M sodium citrate, 0.1 M Na HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.4→48.72 Å / Num. obs: 77041 / % possible obs: 99.6 % / Redundancy: 10.7 % / Rsym value: 0.055 / Net I/σ(I): 21.11
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 10.4 % / Mean I/σ(I) obs: 0.716 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
XSCALEdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1eny

1eny


Resolution: 1.4→40 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.568 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15127 3858 5 %RANDOM
Rwork0.12143 ---
obs0.1229 73178 99.57 %-
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: 31.764 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20.3 Å2-0 Å2
2--0.61 Å2-0 Å2
3----1.98 Å2
Refinement stepCycle: 1 / Resolution: 1.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1994 0 141 266 2401
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0192274
X-RAY DIFFRACTIONr_bond_other_d0.0040.022162
X-RAY DIFFRACTIONr_angle_refined_deg2.1742.0073113
X-RAY DIFFRACTIONr_angle_other_deg1.41934965
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6915286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.75923.83786
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.00915348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0081515
X-RAY DIFFRACTIONr_chiral_restr0.1990.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212694
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02508
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.47911.7041120
X-RAY DIFFRACTIONr_mcbond_other7.44511.6871119
X-RAY DIFFRACTIONr_mcangle_it7.93916.9761414
X-RAY DIFFRACTIONr_mcangle_other7.94816.9871415
X-RAY DIFFRACTIONr_scbond_it23.87415.8321154
X-RAY DIFFRACTIONr_scbond_other23.86715.851155
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other22.37721.0231700
X-RAY DIFFRACTIONr_long_range_B_refined16.38838.4972721
X-RAY DIFFRACTIONr_long_range_B_other16.61537.4292605
X-RAY DIFFRACTIONr_rigid_bond_restr6.53534435
X-RAY DIFFRACTIONr_sphericity_free41.249595
X-RAY DIFFRACTIONr_sphericity_bonded37.6354556
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 264 -
Rwork0.194 5270 -
obs--98.5 %

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