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- PDB-6yuu: Crystal structure of M. tuberculosis InhA inhibited by SKTS1 -

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Basic information

Entry
Database: PDB / ID: 6yuu
TitleCrystal structure of M. tuberculosis InhA inhibited by SKTS1
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 / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / response to antibiotic
Similarity search - Function
Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-F9T / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis CDC1551 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsEltschkner, S. / Schiebel, J. / Kehrein, J. / Le, T.A. / Davoodi, S. / Merget, B. / Weinrich, J.D. / Tonge, P.J. / Engels, B. / Sotriffer, C.A. / Kisker, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB 630 Germany
CitationJournal: Acs Infect Dis. / Year: 2021
Title: A Long Residence Time Enoyl-Reductase Inhibitor Explores an Extended Binding Region with Isoenzyme-Dependent Tautomer Adaptation and Differential Substrate-Binding Loop Closure.
Authors: Eltschkner, S. / Kehrein, J. / Le, T.A. / Davoodi, S. / Merget, B. / Basak, S. / Weinrich, J.D. / Schiebel, J. / Tonge, P.J. / Engels, B. / Sotriffer, C. / Kisker, C.
History
DepositionApr 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 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)31,9699
Polymers30,7261
Non-polymers1,2438
Water5,296294
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)127,87736
Polymers122,9054
Non-polymers4,97332
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z+1/31
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
Buried area22010 Å2
ΔGint-346 kcal/mol
Surface area33780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.524, 95.524, 128.369
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-500-

HOH

21A-607-

HOH

31A-669-

HOH

41A-681-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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
Details: N-terminal His6tag
Source: (gene. exp.) Mycobacterium tuberculosis CDC1551 (bacteria)
Gene: inhA, MT1531 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WGR0, enoyl-[acyl-carrier-protein] reductase (NADH)

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Non-polymers , 5 types, 302 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-F9T / 6-[4-(4-hexyl-2-oxidanyl-phenoxy)phenoxy]pyridin-2-ol


Mass: 379.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H25NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.96 Å3/Da / Density % sol: 58.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4 / Details: 100 mM Tris, pH 8.4 3 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
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: 2.01→47.76 Å / Num. obs: 23730 / % possible obs: 100 % / Redundancy: 19.1 % / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.041 / Net I/σ(I): 15.5
Reflection shellResolution: 2.01→2.12 Å / Rmerge(I) obs: 1.095 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3383 / Rpim(I) all: 0.254 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X23

2x23


Resolution: 2.01→47.7 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.414 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.119 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17798 1216 5.1 %RANDOM
Rwork0.13726 ---
obs0.13938 22432 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.953 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20.28 Å20 Å2
2--0.55 Å2-0 Å2
3----1.79 Å2
Refinement stepCycle: 1 / Resolution: 2.01→47.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1996 0 78 294 2368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0152144
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171956
X-RAY DIFFRACTIONr_angle_refined_deg1.7051.7752925
X-RAY DIFFRACTIONr_angle_other_deg0.5481.7624574
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8445276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1920.82485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34315318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2711514
X-RAY DIFFRACTIONr_chiral_restr0.0810.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212509
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02383
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_it1.4752.6751083
X-RAY DIFFRACTIONr_mcbond_other1.4732.6741082
X-RAY DIFFRACTIONr_mcangle_it2.1034.0031353
X-RAY DIFFRACTIONr_mcangle_other2.1044.0031353
X-RAY DIFFRACTIONr_scbond_it1.8792.8721061
X-RAY DIFFRACTIONr_scbond_other1.8782.8731062
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7784.241567
X-RAY DIFFRACTIONr_long_range_B_refined5.60134.5842520
X-RAY DIFFRACTIONr_long_range_B_other5.35933.6032453
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.01→2.062 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 72 -
Rwork0.241 1594 -
obs--98 %
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)
12.59040.24680.34593.44251.34124.06270.0315-0.0690.28810.0293-0.06840.0236-0.2838-0.15130.03690.0337-0.00990.00530.0694-0.00070.039549.130257.808516.0686
21.9844-0.0942-2.15162.93890.76442.743-0.0621-0.163-0.0659-0.0495-0.0067-0.41470.01060.3720.06880.0238-0.0176-0.01520.18890.06250.096458.073552.656712.7032
32.5701-0.78751.87792.5340.6813.86090.0215-0.14420.12760.1542-0.0955-0.6477-0.19580.33130.0740.0624-0.085-0.09560.20590.10690.225259.300349.049122.4595
40.73230.1233-0.10781.8693-0.00320.15380.0079-0.0236-0.0216-0.16110.0339-0.2242-0.04760.1178-0.04180.0372-0.02340.03890.1329-0.01930.044447.917838.847819.4236
50.65780.2065-0.2790.8201-0.03680.85850.0166-0.01760.02220.04220.0217-0.0393-0.02680.0201-0.03830.00840.01450.00260.04030.00230.011739.308944.039420.8777
62.9844-1.9644-1.25822.5157-0.05922.1165-0.17520.0844-0.1936-0.25290.09250.18050.3274-0.08420.08270.1288-0.04740.01070.1034-0.00260.049636.328240.9367-0.2304
71.18790.14860.53280.98280.30681.9475-0.03450.08770.1003-0.1273-0.0127-0.0769-0.1420.10230.04720.03290.00830.01190.02840.00810.031334.061854.193914.7989
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 31
2X-RAY DIFFRACTION2A32 - 53
3X-RAY DIFFRACTION3A54 - 82
4X-RAY DIFFRACTION4A83 - 137
5X-RAY DIFFRACTION5A138 - 196
6X-RAY DIFFRACTION6A197 - 225
7X-RAY DIFFRACTION7A226 - 269

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