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

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Basic information

Entry
Database: PDB / ID: 6sqd
TitleCrystal structure of M. tuberculosis InhA in complex with NAD+ and 2-pyrazol-1-ylbenzoic 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 / 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
2-pyrazol-1-ylbenzoic 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: 1.72 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)29,4933
Polymers28,6421
Non-polymers8522
Water3,063170
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)117,97412
Polymers114,5674
Non-polymers3,4068
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 area19060 Å2
ΔGint-130 kcal/mol
Surface area33120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.605, 97.605, 139.455
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-441-

HOH

21A-467-

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-LT8 / 2-pyrazol-1-ylbenzoic acid


Mass: 188.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 3.35 Å3/Da / Density % sol: 63.26 %
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: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.719→84.53 Å / Num. obs: 42463 / % possible obs: 100 % / Redundancy: 18.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.014 / Rrim(I) all: 0.061 / Net I/σ(I): 24.8
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.72-1.8117.70.75810793761100.9620.1840.7813
5.43-84.5316.80.0432605215470.9990.0110.04458.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.12 Å84.53 Å
Translation6.12 Å84.53 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.7.1data scaling
PHASER2.8.1phasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B35

2b35


Resolution: 1.72→84.528 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.06
RfactorNum. reflection% reflection
Rfree0.1804 2202 5.19 %
Rwork0.1599 --
obs0.1609 42389 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.42 Å2 / Biso mean: 39.205 Å2 / Biso min: 22.39 Å2
Refinement stepCycle: final / Resolution: 1.72→84.528 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1984 0 58 170 2212
Biso mean--47.4 48.24 -
Num. residues----267
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.72-1.75590.19881310.20152460
1.7559-1.79670.2311370.18912459
1.7967-1.84170.20761270.17332487
1.8417-1.89150.19561310.17442452
1.8915-1.94710.17691540.16892440
1.9471-2.010.19251490.16412462
2.01-2.08180.19061340.15792494
2.0818-2.16520.1721170.16062485
2.1652-2.26370.16981330.15852504
2.2637-2.38310.20811430.16482486
2.3831-2.53240.18671400.1682497
2.5324-2.72790.18531490.16542506
2.7279-3.00250.18371300.16392540
3.0025-3.43690.20911170.16222567
3.4369-4.33020.14481540.14382577
4.3302-84.5280.18181560.15972771
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)
13.43530.2141-0.79791.3008-0.06281.3617-0.0219-0.15330.19560.11260.0205-0.2304-0.32060.50630.0130.4338-0.1912-0.05020.33080.03050.356640.5368-16.517228.9824
23.05790.72430.65010.7030.13880.21730.0349-0.24830.31620.3239-0.19910.009-0.50070.1249-0.05120.6593-0.1665-0.04840.35230.00940.379936.1003-7.829431.6908
31.81211.05230.00411.1287-0.4830.5293-0.17860.13560.5155-0.1770.098-0.0659-0.58560.13730.01520.6642-0.1213-0.05940.27930.02260.399731.2014-6.62921.4516
41.56810.3253-0.1590.94840.07951.32250.0217-0.02410.16630.0251-0.06470.0335-0.3720.0281-0.02480.2902-0.0244-0.03860.190.00360.250223.0471-22.685924.7952
50.6131-0.12630.27560.73180.26971.1010.0286-0.13450.06310.1709-0.09090.0246-0.14260.0870.03820.2916-0.0919-0.01030.3086-0.00790.31232.1762-30.136434.5097
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 31 )A3 - 31
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 53 )A32 - 53
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 82 )A54 - 82
4X-RAY DIFFRACTION4chain 'A' and (resid 83 through 182 )A83 - 182
5X-RAY DIFFRACTION5chain 'A' and (resid 183 through 269 )A183 - 269

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