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- PDB-5ugu: Crystal structure of M. tuberculosis InhA inhibited by PT506 -

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Basic information

Entry
Database: PDB / ID: 5ugu
TitleCrystal structure of M. tuberculosis InhA inhibited by PT506
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / bacterial enoyl-ACP reductase / diphenylether / residence time
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 / 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 / Chem-XTV / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsEltschkner, S. / Pschibul, A. / Spagnuolo, L.A. / Yu, W. / Tonge, P.J. / Kisker, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB 630 Germany
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Evaluating the Contribution of Transition-State Destabilization to Changes in the Residence Time of Triazole-Based InhA Inhibitors.
Authors: Spagnuolo, L.A. / Eltschkner, S. / Yu, W. / Daryaee, F. / Davoodi, S. / Knudson, S.E. / Allen, E.K. / Merino, J. / Pschibul, A. / Moree, B. / Thivalapill, N. / Truglio, J.J. / Salafsky, J. / ...Authors: Spagnuolo, L.A. / Eltschkner, S. / Yu, W. / Daryaee, F. / Davoodi, S. / Knudson, S.E. / Allen, E.K. / Merino, J. / Pschibul, A. / Moree, B. / Thivalapill, N. / Truglio, J.J. / Salafsky, J. / Slayden, R.A. / Kisker, C. / Tonge, P.J.
History
DepositionJan 10, 2017Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 17, 2024Group: 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)31,7223
Polymers30,7261
Non-polymers9962
Water3,135174
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)126,88812
Polymers122,9054
Non-polymers3,9838
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area19260 Å2
ΔGint-123 kcal/mol
Surface area34880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.655, 90.655, 182.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-410-

HOH

21A-450-

HOH

31A-471-

HOH

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Components

#1: Protein Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-ACP reductase / FAS-II enoyl-ACP reductase / NADH-dependent 2-trans-enoyl-ACP reductase


Mass: 30726.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: inhA, Rv1484, MTCY277.05 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WGR1, enoyl-[acyl-carrier-protein] reductase (NADH)
#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-XTV / 2-[4-[(4-cyclopropyl-1,2,3-triazol-1-yl)methyl]-2-oxidanyl-phenoxy]benzenecarbonitrile


Mass: 332.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H16N4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 3.2 Å3/Da / Density % sol: 59.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.4 M sodium acetate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.95→45.72 Å / Num. obs: 28237 / % possible obs: 100 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 14.6
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 12.8 % / Mean I/σ(I) obs: 2 / Num. unique all: 4039 / CC1/2: 0.415 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDS5.8.0073data scaling
XDSdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X23

2x23


Resolution: 1.95→45.72 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.962 / SU B: 7.973 / SU ML: 0.116 / Cross valid method: FREE R-VALUE / ESU R: 0.118 / ESU R Free: 0.124 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21233 1433 5.1 %copy freeR from another mtz
Rwork0.16362 ---
obs0.16608 26782 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 46.055 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å20 Å2
2--0.9 Å2-0 Å2
3----1.79 Å2
Refinement stepCycle: 1 / Resolution: 1.95→45.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1996 0 69 174 2239
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0192183
X-RAY DIFFRACTIONr_bond_other_d0.0030.022107
X-RAY DIFFRACTIONr_angle_refined_deg2.3931.9832982
X-RAY DIFFRACTIONr_angle_other_deg1.223.0024840
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.515284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.4623.82781
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.47315346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8911514
X-RAY DIFFRACTIONr_chiral_restr0.1370.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212581
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02484
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_it1.42.1651112
X-RAY DIFFRACTIONr_mcbond_other1.3922.1621109
X-RAY DIFFRACTIONr_mcangle_it1.9783.2361391
X-RAY DIFFRACTIONr_mcangle_other1.9773.2361391
X-RAY DIFFRACTIONr_scbond_it1.9282.4321071
X-RAY DIFFRACTIONr_scbond_other1.9272.4331072
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9353.5731584
X-RAY DIFFRACTIONr_long_range_B_refined5.91226.8032406
X-RAY DIFFRACTIONr_long_range_B_other5.91226.8032406
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 91 -
Rwork0.332 1960 -
obs--100 %
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)
12.8972-0.6021-1.04242.8474-1.56074.77620.09410.1959-0.2293-0.1673-0.10660.37050.5404-0.7080.01250.1064-0.1741-0.05740.48590.07360.2294-28.8009-9.4891-5.1338
21.1959-1.46461.96867.27760.72525.16010.0917-0.1854-0.0041-0.6872-0.21830.2306-0.1648-0.83950.12660.077-0.0268-0.00560.70110.10130.3709-36.3171-2.0924-8.486
31.44630.4302-0.23631.541-0.07092.32460.13550.0260.1298-0.01470.06890.3667-0.2121-0.868-0.20450.03170.07840.01730.36240.1020.174-23.05795.1459-0.2521
43.1328-0.37220.06971.84970.30913.37560.17490.28850.0542-0.326-0.03680.1060.1147-0.4069-0.1380.0745-0.0301-0.02350.2290.0590.1123-18.8373-2.0237-7.717
510.72721.42125.01885.7255-3.56285.5865-0.33650.1507-0.4249-0.04630.76540.1217-0.1649-0.5741-0.42890.29750.01830.0920.47720.12510.444-17.7669.6039-24.0159
61.0776-1.75220.51363.89440.3071.57510.29440.09510.1566-0.898-0.2165-0.303-0.1723-0.1473-0.07780.3577-0.0912-0.06720.36030.06720.2004-10.0236-2.1483-20.0678
71.5449-0.5968-0.04521.68580.40453.43080.07210.0867-0.05-0.07050.0710.14920.4711-0.5839-0.14310.0829-0.0973-0.05380.13570.06610.0832-13.0228-9.6695-3.5006
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 31
2X-RAY DIFFRACTION2A32 - 53
3X-RAY DIFFRACTION3A54 - 182
4X-RAY DIFFRACTION4A183 - 201
5X-RAY DIFFRACTION5A202 - 208
6X-RAY DIFFRACTION6A209 - 235
7X-RAY DIFFRACTION7A236 - 269

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