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- PDB-9c1d: Mycobaterium tuberculosis Pks13 acyltransferase incubated with DMSO -

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Basic information

Entry
Database: PDB / ID: 9c1d
TitleMycobaterium tuberculosis Pks13 acyltransferase incubated with DMSO
ComponentsPolyketide synthase Pks13
KeywordsANTIBIOTIC / inhibitor / covalent / SuFEx / acyltransferase / Structural Genomics / TB Structural Genomics Consortium / TBSGC
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, active site / Ketosynthase family 3 (KS3) active site signature. / Beta-ketoacyl synthase / 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
DI(HYDROXYETHYL)ETHER / Polyketide synthase Pks13
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsTang, S. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
Funding support United States, 3items
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
CitationJournal: To Be Published
Title: Mycobaterium tuberculosis Pks13 acyltransferase incubated with DMSO
Authors: Tang, S. / Sacchettini, J.C.
History
DepositionMay 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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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
C: Polyketide synthase Pks13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,13760
Polymers159,2243
Non-polymers4,91357
Water9,386521
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A: Polyketide synthase Pks13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,86933
Polymers53,0751
Non-polymers2,79432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-64 kcal/mol
Surface area19780 Å2
MethodPISA
2
B: Polyketide synthase Pks13
C: Polyketide synthase Pks13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,26827
Polymers106,1502
Non-polymers2,11925
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-69 kcal/mol
Surface area20380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.183, 106.183, 259.679
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-1104-

SO4

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Polyketide synthase Pks13


Mass: 53074.770 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: pks13, Rv3800c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: I6X8D2, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

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Non-polymers , 10 types, 578 molecules

#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400


Mass: 398.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#10: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 521 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 3.57 Å3/Da / Density % sol: 65.53 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 1.8 M (NH)4SO4, 4%-6% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 93969 / % possible obs: 100 % / Redundancy: 12.1 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.027 / Rrim(I) all: 0.096 / Χ2: 0.959 / Net I/σ(I): 5.9 / Num. measured all: 1139148
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.05-2.0911.40.99146580.8630.9630.2951.0350.734100
2.09-2.1211.90.79546130.9220.980.2330.8290.746100
2.12-2.1612.10.73946110.9460.9860.2170.7710.746100
2.16-2.2112.20.62446310.950.9870.1830.6510.739100
2.21-2.26120.51446290.9640.9910.1530.5360.771100
2.26-2.31110.46646380.9610.990.1450.4880.776100
2.31-2.3712.20.39846050.9770.9940.1170.4150.787100
2.37-2.4312.60.34846540.980.9950.10.3630.802100
2.43-2.512.50.29546670.9850.9960.0850.3070.826100
2.5-2.5812.30.24546450.9880.9970.0710.2550.848100
2.58-2.6812.10.21446470.9910.9980.0630.2230.872100
2.68-2.7811.60.17946760.9920.9980.0540.1870.92399.9
2.78-2.9111.70.14146690.9950.9990.0420.1470.986100
2.91-3.0612.50.11247040.9970.9990.0320.1171.046100
3.06-3.2512.50.0947050.9980.9990.0260.0941.125100
3.25-3.5112.40.07347130.99810.0220.0771.243100
3.51-3.8611.80.06247480.99810.0190.0641.34100
3.86-4.4213.10.05348010.99810.0150.0551.347100
4.42-5.5612.20.04948320.99910.0150.0521.22799.9
5.56-5012.40.04451230.99910.0130.0461.15999.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
SCALEPACKdata scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→49.14 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2214 2757 2.96 %
Rwork0.1914 --
obs0.1923 93267 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→49.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7170 0 291 521 7982
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.569
X-RAY DIFFRACTIONf_dihedral_angle_d13.0452756
X-RAY DIFFRACTIONf_chiral_restr0.0421141
X-RAY DIFFRACTIONf_plane_restr0.0061324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.080.34621360.29454381X-RAY DIFFRACTION97
2.08-2.120.29851320.25784393X-RAY DIFFRACTION98
2.12-2.160.26731330.23814420X-RAY DIFFRACTION99
2.16-2.210.23721370.22964430X-RAY DIFFRACTION99
2.21-2.260.24491350.21284449X-RAY DIFFRACTION99
2.26-2.310.22821340.21364469X-RAY DIFFRACTION99
2.31-2.370.22011370.21324427X-RAY DIFFRACTION99
2.37-2.430.22841320.21244485X-RAY DIFFRACTION99
2.43-2.50.2551410.2174495X-RAY DIFFRACTION99
2.5-2.580.24741380.21744480X-RAY DIFFRACTION99
2.58-2.670.24881330.21044491X-RAY DIFFRACTION100
2.67-2.780.2481330.20394539X-RAY DIFFRACTION100
2.78-2.910.22981440.20584506X-RAY DIFFRACTION100
2.91-3.060.2591380.21194555X-RAY DIFFRACTION100
3.06-3.250.25261380.20894561X-RAY DIFFRACTION100
3.25-3.50.24671460.19684559X-RAY DIFFRACTION100
3.5-3.860.22261350.18284609X-RAY DIFFRACTION100
3.86-4.410.19061390.1524655X-RAY DIFFRACTION100
4.41-5.560.16941450.15974679X-RAY DIFFRACTION100
5.56-49.140.18571510.17384927X-RAY DIFFRACTION100

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