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- PDB-8otl: structure of InhA from Mycobacterium tuberculosis in complex with... -

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Basic information

Entry
Database: PDB / ID: 8otl
Titlestructure of InhA from Mycobacterium tuberculosis in complex with 5-(((4-(2-hydroxyphenoxy)benzyl)(octyl)amino)methyl)-2-phenoxyphenol
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / enoyl-ACP-reductase type II fatty acid synthase mycolic acids tuberculosis therapeutic target
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 domain superfamily
Similarity search - Domain/homology
ACETATE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-VZE / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.108 Å
AuthorsTamhaev, R. / Maveyraud, L. / Chebaiki, M. / Lherbet, C. / Mourey, L.
Funding support France, 3items
OrganizationGrant numberCountry
Universite de Toulouse France
La Region Occitanie France
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Bioorg.Chem. / Year: 2023
Title: Exploring the plasticity of the InhA substrate-binding site using new diaryl ether inhibitors.
Authors: Tamhaev, R. / Grosjean, E. / Ahamed, H. / Chebaiki, M. / Rodriguez, F. / Recchia, D. / Degiacomi, G. / Pasca, M.R. / Maveyraud, L. / Mourey, L. / Lherbet, C.
History
DepositionApr 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release

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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)177,77117
Polymers173,0226
Non-polymers4,74811
Water8,935496
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)118,0028
Polymers115,3484
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area18720 Å2
ΔGint-133 kcal/mol
Surface area33280 Å2
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)118,77013
Polymers115,3484
Non-polymers3,4229
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19650 Å2
ΔGint-119 kcal/mol
Surface area32950 Å2
Unit cell
Length a, b, c (Å)80.85, 100.875, 376.071
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 6 molecules ABCDEF

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


Mass: 28837.057 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: inhA, Rv1484, MTCY277.05
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P9WGR1, enoyl-[acyl-carrier-protein] reductase (NADH)

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Non-polymers , 5 types, 507 molecules

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


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-VZE / 5-[[octyl-[[4-(2-oxidanylphenoxy)phenyl]methyl]amino]methyl]-2-phenoxy-phenol


Mass: 525.678 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H39NO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 496 / 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: 2.24 Å3/Da / Density % sol: 45.03 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 14 % PEG 4000 100 mM ADA 100 mM acetate ammonium, pH 6.8, 5 % DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 5, 2022
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.108→62.218 Å / Num. obs: 84677 / % possible obs: 95 % / Redundancy: 8.89 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.996 / CC1/2 anomalous: -0.078 / Rmerge(I) obs: 0.1649 / Rpim(I) all: 0.0575 / Rrim(I) all: 0.1753 / AbsDiff over sigma anomalous: 0.767 / Net I/σ(I): 9.73 / Num. measured all: 752360 / % possible anomalous: 94.4 / Redundancy anomalous: 4.67
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalousRedundancy anomalous% possible all
5.72-62.2188.170.063322.113803038030465246520.998-0.0940.02250.06740.70898.14.6498.3
4.54-5.728.410.080920.53786437864450245020.997-0.1460.0290.08620.7598.44.5599
3.967-4.548.960.07922.074029440294449744970.997-0.090.02740.08380.72999.14.7799.1
3.604-3.9678.680.097518.583111031110358635860.995-0.1660.03440.10370.75580.74.5980.8
3.346-3.6048.960.122315.984030540305449744970.993-0.1070.04250.12990.79399.34.7299.6
3.148-3.3469.090.155313.394029240292443544350.99-0.0780.05340.16470.76499.34.7699.6
2.991-3.1489.310.200510.914139841398444744470.985-0.110.06820.21250.79499.24.8999.9
2.861-2.9919.340.22979.734165041650445944590.979-0.0580.07750.24320.78199.64.88100
2.75-2.8618.940.27048.173965139651443544350.972-0.0290.09410.28720.79299.64.6599.9
2.656-2.759.160.31637.124046940469441944190.9570.0130.10920.33570.80999.84.7699.9
2.573-2.6568.680.35136.193796437964437643760.948-0.0320.12450.37390.78499.24.5399.9
2.499-2.5739.080.41075.434036840368444444440.929-0.0140.14220.43590.77399.64.7299.9
2.433-2.4999.240.44525.114098040980443444340.903-0.0180.15310.47220.77699.74.79100
2.374-2.4339.260.46264.914082240822440944090.9050.0060.15930.49070.78799.84.79100
2.32-2.3749.290.51534.394082940829439443940.877-0.040.17710.54650.76999.74.81100
2.271-2.328.780.56423.833898338983444244420.851-0.0160.19970.60030.75799.64.54100
2.225-2.2715.750.64272.4659275927103010300.670.0510.27510.70450.75720.53.323.6
2.183-2.2258.880.68393.183936139361443344330.789-0.0140.240.7270.76599.14.6199.8
2.144-2.1838.620.73962.873746237462434843480.792-0.0050.2640.78750.73399.24.4699.9
2.108-2.1448.70.87652.433860138601443844380.673-0.040.30980.93260.742984.5399.2

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (8-JUN-2022)refinement
autoPROC1.0.5 20220608data processing
XDSJan 10, 2022data reduction
Aimless0.7.9data scaling
MOLREP11.9.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.108→30.65 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.916 / SU R Cruickshank DPI: 0.259 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.261 / SU Rfree Blow DPI: 0.194 / SU Rfree Cruickshank DPI: 0.196
RfactorNum. reflection% reflectionSelection details
Rfree0.2373 4373 -RANDOM
Rwork0.1998 ---
obs0.2018 84639 95 %-
Displacement parametersBiso mean: 31.57 Å2
Baniso -1Baniso -2Baniso -3
1--1.8074 Å20 Å20 Å2
2--2.4249 Å20 Å2
3----0.6175 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 2.108→30.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11603 0 319 496 12418
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00812371HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9416900HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4095SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2173HARMONIC5
X-RAY DIFFRACTIONt_it12371HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1688SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies19HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact11060SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.34
X-RAY DIFFRACTIONt_other_torsion16.57
LS refinement shellResolution: 2.11→2.12 Å
RfactorNum. reflection% reflection
Rfree0.2827 82 -
Rwork0.2602 --
obs0.2613 1693 99.48 %
Refinement TLS params.

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)
10.4888-0.10840.05561.4269-0.18850.8058-0.0328-0.217-0.1114-0.2170.05330.0717-0.11140.0717-0.02040.0104-0.05840.0111-0.06780.0241-0.07385.043523.478578.6365
20.6435-0.1586-0.32591.5237-0.0090.9743-0.0798-0.33070.1917-0.33070.0695-0.14570.1917-0.14570.01030.0457-0.076-0.0235-0.0628-0.0179-0.0965-4.8095-6.707378.7253
30.6890.1284-0.09890.8807-0.16661.0829-0.0188-0.15730.1091-0.15730.023-0.08120.1091-0.0812-0.0042-0.0282-0.0299-0.0042-0.0543-0.0039-0.0677-4.429436.649311.6799
40.76990.41470.17120.91940.00740.85350.01470.14480.00830.14480.0063-0.19060.0083-0.1906-0.021-0.0439-0.02260.0182-0.04180.0236-0.0468-18.85440.131340.3473
51.59560.3236-0.26981.0548-0.24050.79870.06010.3046-0.24980.3046-0.07080.0956-0.24980.09560.01060.0504-0.0628-0.0616-0.1002-0.0188-0.05956.633157.852947.5747
60.95770.09040.03880.9617-0.30491.3049-0.02630.02760.09440.0276-0.10020.27830.09440.27830.1265-0.1150.0032-0.0244-0.06360.04980.084422.859836.692929.1654
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 269
2X-RAY DIFFRACTION1{ A|* }A301
3X-RAY DIFFRACTION2{ B|* }B3 - 269
4X-RAY DIFFRACTION2{ B|* }B301
5X-RAY DIFFRACTION3{ C|* }C3 - 269
6X-RAY DIFFRACTION3{ C|* }C301 - 302
7X-RAY DIFFRACTION4{ D|* }D3 - 269
8X-RAY DIFFRACTION4{ D|* }D301 - 303
9X-RAY DIFFRACTION5{ E|* }E3 - 269
10X-RAY DIFFRACTION5{ E|* }E301 - 302
11X-RAY DIFFRACTION6{ F|* }F2 - 269
12X-RAY DIFFRACTION6{ F|* }F301 - 302

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