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- PDB-8tqv: Crystal Structure of Mtb Pks13 Thioesterase domain in complex wit... -

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Basic information

Entry
Database: PDB / ID: 8tqv
TitleCrystal Structure of Mtb Pks13 Thioesterase domain in complex with inhibitor X20403
ComponentsPolyketide synthase Pks13
KeywordsBIOSYNTHETIC PROTEIN / polyketide synthase / thioesterase
Function / homology
Function and homology information


DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / fatty acid biosynthetic process / cytoplasm
Similarity search - Function
: / Thioesterase / Thioesterase domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. ...: / Thioesterase / Thioesterase domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
: / Polyketide synthase Pks13
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKrieger, I.V. / Sacchettini, J.C.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI095208 United States
Welch FoundationA-0015 United States
Bill & Melinda Gates FoundationINV-040487 United States
Department of Defense (DOD, United States)W81XWH-17-1-0692 United States
CitationJournal: Acs Infect Dis. / Year: 2024
Title: Inhibitors of the Thioesterase Activity of Mycobacterium tuberculosis Pks13 Discovered Using DNA-Encoded Chemical Library Screening.
Authors: Krieger, I.V. / Yalamanchili, S. / Dickson, P. / Engelhart, C.A. / Zimmerman, M.D. / Wood, J. / Clary, E. / Nguyen, J. / Thornton, N. / Centrella, P.A. / Chan, B. / Cuozzo, J.W. / ...Authors: Krieger, I.V. / Yalamanchili, S. / Dickson, P. / Engelhart, C.A. / Zimmerman, M.D. / Wood, J. / Clary, E. / Nguyen, J. / Thornton, N. / Centrella, P.A. / Chan, B. / Cuozzo, J.W. / Gengenbacher, M. / Guie, M.A. / Guilinger, J.P. / Bienstock, C. / Hartl, H. / Hupp, C.D. / Jetson, R. / Satoh, T. / Yeoman, J.T.S. / Zhang, Y. / Dartois, V. / Schnappinger, D. / Keefe, A.D. / Sacchettini, J.C.
History
DepositionAug 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyketide synthase Pks13
B: Polyketide synthase Pks13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7618
Polymers61,2932
Non-polymers1,4686
Water1,63991
1
A: Polyketide synthase Pks13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3804
Polymers30,6471
Non-polymers7343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polyketide synthase Pks13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3804
Polymers30,6471
Non-polymers7343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.564, 84.505, 124.703
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein Polyketide synthase Pks13


Mass: 30646.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: pks13 / Production host: Escherichia coli (E. coli)
References: UniProt: I6X8D2, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-JS9 / 4-(2-{(4M)-4-[(6M)-6-(2,5-dimethoxyphenyl)pyridin-3-yl]-1H-1,2,3-triazol-1-yl}ethyl)-N-{[1-(methoxymethyl)cyclopropyl]methyl}-N-methylbenzamide


Mass: 541.641 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H35N5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.84 Å3/Da / Density % sol: 56.76 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M TRIS-HCL, 2.0-1.8 M AMMONIUM SULFATE, 2%-5% V/V PPG P400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2→47.49 Å / Num. obs: 46267 / % possible obs: 98.9 % / Redundancy: 5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.032 / Net I/σ(I): 10.4
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.128 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3415 / CC1/2: 0.644 / Rpim(I) all: 0.569 / % possible all: 99.9

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Processing

Software
NameClassification
PDB-REDOrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→47.49 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / SU B: 13.536 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24587 2277 4.9 %RANDOM
Rwork0.22412 ---
obs0.22518 43951 98.56 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.194 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-0 Å2-0 Å2
2--0.05 Å2-0 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 2→47.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4218 0 100 91 4409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0164417
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163997
X-RAY DIFFRACTIONr_angle_refined_deg0.8861.8216002
X-RAY DIFFRACTIONr_angle_other_deg0.3291.5839283
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3545.356576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.76610690
X-RAY DIFFRACTIONr_chiral_restr0.0420.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025129
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02893
X-RAY DIFFRACTIONr_mcbond_it2.9672.9982152
X-RAY DIFFRACTIONr_mcbond_other2.9652.9992152
X-RAY DIFFRACTIONr_mcangle_it4.1324.4742683
X-RAY DIFFRACTIONr_mcangle_other4.1314.4762684
X-RAY DIFFRACTIONr_scbond_it4.123.5212265
X-RAY DIFFRACTIONr_scbond_other3.93.4752250
X-RAY DIFFRACTIONr_scangle_other5.5955.0673290
X-RAY DIFFRACTIONr_long_range_B_refined838.7534879
X-RAY DIFFRACTIONr_long_range_B_other8.00238.6844872
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 180 -
Rwork0.375 3227 -
obs--99.91 %
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)
13.59150.518-0.65331.48120.44492.25560.19990.1305-0.0523-0.1851-0.3576-0.0081-0.0927-0.14960.15760.41910.1297-0.01420.18170.02570.0492.366-12.08914.626
21.10650.56350.06945.5397-0.8051.5467-0.3436-0.11890.02450.78080.428-0.2226-0.0229-0.1289-0.08450.57470.2348-0.01640.2687-0.04750.053-20.727-45.1616.405
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1454 - 1726
2X-RAY DIFFRACTION2B1452 - 1726

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