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- PDB-6sqb: Crystal structure of M. tuberculosis InhA in complex with NAD+ an... -

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Basic information

Entry
Database: PDB / ID: 6sqb
TitleCrystal structure of M. tuberculosis InhA in complex with NAD+ and 3-(3-chlorophenyl)propanoic acid
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / InhA / NADH-dependent enoyl-[acyl-carrier-protein] reductase
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
3-(3-chlorophenyl)propanoic acid / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.774 Å
AuthorsMendes, V. / Sabbah, M. / Coyne, A.G. / Abell, C. / Blundell, T.L.
Funding support United Kingdom, United States, 2items
OrganizationGrant numberCountry
European Communitys Seventh Framework Programme260872 United Kingdom
Bill & Melinda Gates FoundationOPP1158806 United States
CitationJournal: J.Med.Chem. / Year: 2020
Title: Fragment-Based Design ofMycobacterium tuberculosisInhA Inhibitors.
Authors: Sabbah, M. / Mendes, V. / Vistal, R.G. / Dias, D.M.G. / Zahorszka, M. / Mikusova, K. / Kordulakova, J. / Coyne, A.G. / Blundell, T.L. / Abell, C.
History
DepositionSep 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 27, 2020Group: 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 1.3Jan 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,7284
Polymers28,6421
Non-polymers1,0863
Water3,891216
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)118,91316
Polymers114,5674
Non-polymers4,34512
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 area20380 Å2
ΔGint-109 kcal/mol
Surface area33910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.829, 97.829, 140.590
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-466-

HOH

21A-493-

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: 28641.857 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: inhA, Rv1484, MTCY277.05 / Production host: Escherichia coli BL21(DE3) (bacteria)
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-LSQ / 3-(3-chlorophenyl)propanoic acid


Mass: 184.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9ClO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O
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: 3.39 Å3/Da / Density % sol: 63.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES pH 7.0 0.1 M sodium acetate 25-30% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.77→84.722 Å / Num. obs: 39125 / % possible obs: 99.9 % / Redundancy: 26.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.017 / Rrim(I) all: 0.087 / Net I/σ(I): 28.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.77-2.0527.20.77365696134270.970.1490.7854.8100
3.55-84.7223.70.03712425052320.9990.0080.03881.599.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.13 Å84.72 Å
Translation6.13 Å84.72 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.2.17data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B35

2b35


Resolution: 1.774→84.72 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.73
RfactorNum. reflection% reflection
Rfree0.1737 1919 4.91 %
Rwork0.1559 --
obs0.1567 39069 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 105.24 Å2 / Biso mean: 32.9959 Å2 / Biso min: 15.77 Å2
Refinement stepCycle: final / Resolution: 1.774→84.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1988 0 71 216 2275
Biso mean--43.83 45 -
Num. residues----267
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.774-1.81830.27931230.25452611100
1.8183-1.86750.22961450.21572557100
1.8675-1.92240.21021210.19492636100
1.9224-1.98450.20361390.17612596100
1.9845-2.05540.20631580.16012584100
2.0554-2.13770.17661310.16272638100
2.1377-2.2350.17831540.1512602100
2.235-2.35280.17981420.15272624100
2.3528-2.50030.1791380.15262627100
2.5003-2.69330.17221100.15242670100
2.6933-2.96440.14761320.15062681100
2.9644-3.39330.14651340.15322702100
3.3933-4.27520.15481460.13972723100
4.2752-84.720.18671460.1553289999
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)
11.65150.2957-0.05341.1431-0.00141.05270.0043-0.0330.1590.0417-0.05510.0341-0.32620.0159-0.01180.2151-0.0133-0.04580.12250.00060.166723.4558-22.691124.3948
20.94750.10120.13910.97180.20291.08560.0218-0.15750.07490.1864-0.10070.0261-0.09240.02730.03930.2141-0.0602-0.02060.216-0.00890.2232.3469-30.30234.7792
32.5939-0.0956-0.33491.3671-0.12160.9078-0.0306-0.01870.33550.19690.0032-0.2353-0.32430.3410.04560.3417-0.1456-0.07230.24890.03740.291840.6691-16.577929.1988
43.50370.77410.23570.95470.07650.18240.0351-0.27270.39850.3395-0.1685-0.095-0.38910.11570.03370.5246-0.147-0.07830.26580.01530.289936.3257-7.88431.9505
51.2350.4161-0.07591.053-0.87420.8802-0.22530.12690.5034-0.08050.0860.0111-0.52960.13590.05910.5409-0.1011-0.08380.2340.01430.340331.5603-6.575721.8991
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 83 through 182 )A83 - 182
2X-RAY DIFFRACTION2chain 'A' and (resid 183 through 269 )A183 - 269
3X-RAY DIFFRACTION3chain 'A' and (resid 3 through 31 )A3 - 31
4X-RAY DIFFRACTION4chain 'A' and (resid 32 through 53 )A32 - 53
5X-RAY DIFFRACTION5chain 'A' and (resid 54 through 82 )A54 - 82

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