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- PDB-2x23: crystal structure of M. tuberculosis InhA inhibited by PT70 -

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Basic information

Entry
Database: PDB / ID: 2x23
Titlecrystal structure of M. tuberculosis InhA inhibited by PT70
ComponentsENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
KeywordsOXIDOREDUCTASE / FATTY ACID BIOSYNTHESIS / LIPID SYNTHESIS / ANTIBIOTIC RESISTANCE
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase [NAD(P)H] activity / 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 [NAD(P)H] activity / 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 / 5-HEXYL-2-(2-METHYLPHENOXY)PHENOL / Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.807 Å
AuthorsLuckner, S.R. / Liu, N. / am Ende, C.W. / Tonge, P.J. / Kisker, C.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: A Slow, Tight Binding Inhibitor of Inha, the Enoyl-Acyl Carrier Protein Reductase from Mycobacterium Tuberculosis.
Authors: Luckner, S.R. / Liu, N. / Am Ende, C.W. / Tonge, P.J. / Kisker, C.
History
DepositionJan 10, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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]
E: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
G: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,08913
Polymers114,2194
Non-polymers3,8699
Water12,286682
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22040 Å2
ΔGint-146.1 kcal/mol
Surface area33390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.480, 90.270, 89.560
Angle α, β, γ (deg.)90.00, 118.76, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.2445, 0.96496, -0.0952), (0.96792, 0.23702, -0.08345), (-0.05796, -0.11255, -0.99195)-9.3546, 4.4115, -36.10949
2given(-0.2445, 0.96496, -0.0952), (0.96792, 0.23702, -0.08345), (-0.05796, -0.11255, -0.99195)-9.3546, 4.4115, -36.10949
3given(0.23787, -0.97121, 0.0127), (-0.97112, -0.23805, -0.01581), (0.01838, -0.00857, -0.99979)-37.7084, -48.44903, -32.31175

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Components

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


Mass: 28554.781 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS
References: UniProt: P0A5Y6, UniProt: P9WGR1*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-TCU / 5-HEXYL-2-(2-METHYLPHENOXY)PHENOL / 2-(O-TOLYLOXY)-5-HEXYLPHENOL


Mass: 284.393 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H24O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 682 / 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: 2.8 Å3/Da / Density % sol: 56.09 % / Description: NONE
Crystal growDetails: 12-16% (W/V) PEG 4000, 1% DMSO, 250MM AMMONIUM ACETATE, 100MM ADA PH 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Sep 5, 2007 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.81→78.57 Å / Num. obs: 112937 / % possible obs: 92.5 % / Observed criterion σ(I): 2 / Redundancy: 1.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.1
Reflection shellResolution: 1.81→1.9 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.7 / % possible all: 77.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.807→78.567 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.589 / SU ML: 0.076 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.114 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.203 5469 5 %RANDOM
Rwork0.1676 ---
obs0.169 108944 96.529 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 10.641 Å2
Baniso -1Baniso -2Baniso -3
1-0.196 Å20 Å20.201 Å2
2---0.171 Å20 Å2
3---0.169 Å2
Refinement stepCycle: LAST / Resolution: 1.807→78.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7980 0 264 682 8926
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228480
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5342.00511555
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.14651092
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41623.918319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.443151342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2731553
X-RAY DIFFRACTIONr_chiral_restr0.1050.21321
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026333
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.24278
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.25833
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2676
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8731.55504
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2328514
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.11533465
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2254.53029
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.807→1.854 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 367 -
Rwork0.233 6437 -
obs--82.253 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8672-0.1288-0.06550.83210.06070.65760.01140.02630.103-0.0403-0.0080.0187-0.0794-0.0279-0.0034-0.07380.00450.0016-0.07760.0069-0.0926-25.7390.1462-22.4136
21.1329-0.06120.14411.24570.02340.33230.0023-0.0990.02490.12140.005-0.07760.01130.0452-0.0073-0.0809-0.0074-0.0125-0.062-0.0064-0.0959-0.7907-18.5957-12.4004
30.8239-0.11830.1210.7482-0.0580.56750.00650.0485-0.0677-0.04930.0009-0.01810.06080.0184-0.0074-0.0707-0.0077-0.0037-0.0806-0.0053-0.1091-20.0821-42.9978-20.5345
40.8939-0.0401-0.05061.2775-0.09010.4278-0.0018-0.1377-0.01340.15010.00910.1209-0.0148-0.0838-0.0074-0.0747-0.00120.0252-0.03660.0084-0.0631-44.2702-23.1208-10.3812
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 269
2X-RAY DIFFRACTION2B2 - 269
3X-RAY DIFFRACTION3E2 - 269
4X-RAY DIFFRACTION4G2 - 269

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