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- PDB-7svt: Mycobacterium tuberculosis 3-hydroxyl-ACP dehydratase HadAB in co... -

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Basic information

Entry
Database: PDB / ID: 7svt
TitleMycobacterium tuberculosis 3-hydroxyl-ACP dehydratase HadAB in complex with 1,3-diarylpyrazolyl-acylsulfonamide inhibitor
Components
  • (3R)-hydroxyacyl-ACP dehydratase subunit HadB
  • HadA
KeywordsLYASE/INHIBITOR / Mycobacterium tuberculosis / Tuberculosis drug discovery / 3-hydroxyl-ACP dehydratase / HadAB/BC / Structural Genomics / TB Structural Genomics Consortium / TBSGC / lipid binding protein / LYASE-INHIBITOR complex
Function / homology
Function and homology information


hydro-lyase activity
Similarity search - Function
Dehydratase subunit HadA-like / : / N-terminal of MaoC-like dehydratase / N-terminal half of MaoC dehydratase / MaoC-like dehydratase domain / MaoC like domain / HotDog domain superfamily
Similarity search - Domain/homology
Chem-CI7 / DI(HYDROXYETHYL)ETHER / UPF0336 protein A4S10_00677 / (3R)-hydroxyacyl-ACP dehydratase subunit HadB
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKrieger, I.V. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Acs Infect Dis. / Year: 2022
Title: 1,3-Diarylpyrazolyl-acylsulfonamides Target HadAB/BC Complex in Mycobacterium tuberculosis .
Authors: Singh, V. / Grzegorzewicz, A.E. / Fienberg, S. / Muller, R. / Khonde, L.P. / Sanz, O. / Alfonso, S. / Urones, B. / Drewes, G. / Bantscheff, M. / Ghidelli-Disse, S. / Ioerger, T.R. / Angala, ...Authors: Singh, V. / Grzegorzewicz, A.E. / Fienberg, S. / Muller, R. / Khonde, L.P. / Sanz, O. / Alfonso, S. / Urones, B. / Drewes, G. / Bantscheff, M. / Ghidelli-Disse, S. / Ioerger, T.R. / Angala, B. / Liu, J. / Lee, R.E. / Sacchettini, J.C. / Krieger, I.V. / Jackson, M. / Chibale, K. / Ghorpade, S.R.
History
DepositionNov 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HadA
B: (3R)-hydroxyacyl-ACP dehydratase subunit HadB
H: HadA
I: (3R)-hydroxyacyl-ACP dehydratase subunit HadB
O: HadA
P: (3R)-hydroxyacyl-ACP dehydratase subunit HadB
V: HadA
W: (3R)-hydroxyacyl-ACP dehydratase subunit HadB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,14917
Polymers129,7908
Non-polymers2,3609
Water1,58588
1
A: HadA
B: (3R)-hydroxyacyl-ACP dehydratase subunit HadB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9924
Polymers32,4472
Non-polymers5452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-18 kcal/mol
Surface area12890 Å2
MethodPISA
2
H: HadA
I: (3R)-hydroxyacyl-ACP dehydratase subunit HadB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9303
Polymers32,4472
Non-polymers4831
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-15 kcal/mol
Surface area12710 Å2
MethodPISA
3
O: HadA
P: (3R)-hydroxyacyl-ACP dehydratase subunit HadB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2356
Polymers32,4472
Non-polymers7874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-13 kcal/mol
Surface area12590 Å2
MethodPISA
4
V: HadA
W: (3R)-hydroxyacyl-ACP dehydratase subunit HadB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9924
Polymers32,4472
Non-polymers5452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-12 kcal/mol
Surface area12920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.298, 107.197, 142.066
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 8 molecules AHOVBIPW

#1: Protein
HadA


Mass: 17497.449 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A045H4M9
#2: Protein
(3R)-hydroxyacyl-ACP dehydratase subunit HadB


Mass: 14949.993 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: A0A045H5L3, Lyases; Carbon-oxygen lyases; Hydro-lyases

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Non-polymers , 5 types, 97 molecules

#3: Chemical
ChemComp-CI7 / 3-[1-(4-bromophenyl)-3-(4-chlorophenyl)-1H-pyrazol-4-yl]-N-(methanesulfonyl)propanamide


Mass: 482.779 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H17BrClN3O3S / Feature type: SUBJECT OF INVESTIGATION
#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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.5 Å3/Da / Density % sol: 50.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: 0.1 M citric acid, pH 3.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→48.64 Å / Num. obs: 51577 / % possible obs: 99.9 % / Redundancy: 5.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.088 / Rrim(I) all: 0.217 / Net I/σ(I): 7.5 / Num. measured all: 299707 / Scaling rejects: 208
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
2.4-2.4761.9622637544220.5360.8592.1461.2100
9.9-48.645.30.04143088120.9980.0190.04623.897.7

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4rlw

4rlw


Resolution: 2.4→45.38 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2751 2568 4.99 %
Rwork0.2173 48902 -
obs0.2203 51470 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159.8 Å2 / Biso mean: 53.7115 Å2 / Biso min: 22.18 Å2
Refinement stepCycle: final / Resolution: 2.4→45.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8976 0 140 88 9204
Biso mean--47.7 45.22 -
Num. residues----1176
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.450.46511240.356327212845100
2.45-2.50.41581570.353926602817100
2.5-2.550.40751450.323626702815100
2.55-2.610.3441360.304126712807100
2.61-2.670.31771320.284827162848100
2.67-2.750.34881490.280526902839100
2.75-2.830.34521280.257126862814100
2.83-2.920.34551280.261827252853100
2.92-3.020.33321590.247326602819100
3.02-3.140.32071380.247627102848100
3.14-3.290.28961450.231627182863100
3.29-3.460.28021340.234627222856100
3.46-3.680.29721330.206127332866100
3.68-3.960.25731570.206127252882100
3.96-4.360.21971390.180527252864100
4.36-4.990.23321590.16422728288799
4.99-6.280.22451440.17732784292899
6.28-45.380.20151610.16682858301998

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