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- PDB-9c9o: M. tuberculosis PKS13 acyltransferase (AT) domain in complex with... -

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Basic information

Entry
Database: PDB / ID: 9c9o
TitleM. tuberculosis PKS13 acyltransferase (AT) domain in complex with SuFEx inhibitor CMX410 - reaction product
Components(Polyketide synthase ...) x 2
KeywordsTRANSFERASE / polyketide synthase / acyltransferase domain / inhibitor / mycobacteria / 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
sucrose / : / Polyketide synthase Pks13
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsKrieger, I.V. / Tang, S. / Sacchetini, 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
Bill & Melinda Gates FoundationINV-040487 United States
Welch FoundationA-0015 United States
CitationJournal: To Be Published
Title: A SuFEx-based TB clinical candidate irreversibly inhibits Pks13
Authors: Krieger, I.V. / Sacchetini, J.C.
History
DepositionJun 14, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 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)170,35417
Polymers166,6203
Non-polymers3,73314
Water7,999444
1
A: Polyketide synthase Pks13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3578
Polymers55,5271
Non-polymers1,8307
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polyketide synthase Pks13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4508
Polymers55,5461
Non-polymers1,9047
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Polyketide synthase Pks13


Theoretical massNumber of molelcules
Total (without water)55,5461
Polymers55,5461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.673, 106.673, 258.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-1101-

SO4

21A-1344-

HOH

31B-1221-

HOH

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Components

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Polyketide synthase ... , 2 types, 3 molecules ABC

#1: Protein Polyketide synthase Pks13


Mass: 55527.441 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: pks13, Rv3800c / Production host: Escherichia coli (E. coli)
References: UniProt: I6X8D2, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Protein Polyketide synthase Pks13


Mass: 55546.441 Da / Num. of mol.: 2
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 (E. coli)
References: UniProt: I6X8D2, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

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Sugars , 1 types, 7 molecules

#3: Polysaccharide
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 451 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-A1AVL / 4-({2,6-difluoro-4-[3-(methanesulfonamido)-1H-1,2,4-triazol-1-yl]phenyl}methoxy)phenyl hydrogen sulfate


Mass: 476.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H14F2N4O7S2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 444 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsThe authors state that the chain C short peptide is part of the ordered N-terminal part of either ...The authors state that the chain C short peptide is part of the ordered N-terminal part of either chain A or chain B, but because of how much is missing, they cannot say whether is it from chain A or chain B.
Has ligand of interestY
Has protein modificationY

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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: 3.59 Å3/Da / Density % sol: 65.78 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.5, 1.7 M (NH4)2SO4, 4-6% PEG 400

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920105 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920105 Å / Relative weight: 1
ReflectionResolution: 2.019→98.62 Å / Num. obs: 79459 / % possible obs: 92.6 % / Redundancy: 7 % / Biso Wilson estimate: 31.34 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.051 / Net I/σ(I): 10.5
Reflection shellResolution: 2.019→2.163 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.324 / Num. unique obs: 3973 / CC1/2: 0.579 / Rpim(I) all: 0.561 / % possible all: 67.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→52.24 Å / SU ML: 0.2437 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5167
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.231 3980 5.01 %
Rwork0.1937 75465 -
obs0.1956 79445 80.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.25 Å2
Refinement stepCycle: LAST / Resolution: 2.02→52.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7172 0 244 444 7860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00727589
X-RAY DIFFRACTIONf_angle_d0.913810319
X-RAY DIFFRACTIONf_chiral_restr0.05091196
X-RAY DIFFRACTIONf_plane_restr0.0081314
X-RAY DIFFRACTIONf_dihedral_angle_d14.12081098
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.040.386410.313813X-RAY DIFFRACTION0.43
2.04-2.070.306690.3163150X-RAY DIFFRACTION4.7
2.07-2.10.4248310.2737561X-RAY DIFFRACTION17.19
2.1-2.130.3208560.27521150X-RAY DIFFRACTION34.7
2.13-2.160.3118900.26991529X-RAY DIFFRACTION46.94
2.16-2.190.31641120.2591902X-RAY DIFFRACTION57.82
2.19-2.220.30341130.25392340X-RAY DIFFRACTION70.57
2.22-2.240.3375670.26261475X-RAY DIFFRACTION74.71
2.26-2.30.28881280.24662491X-RAY DIFFRACTION89.02
2.3-2.340.30441570.2423231X-RAY DIFFRACTION97.47
2.34-2.380.29781790.25053283X-RAY DIFFRACTION99.91
2.38-2.430.29091810.24153355X-RAY DIFFRACTION100
2.43-2.490.25291850.22783284X-RAY DIFFRACTION99.97
2.49-2.540.29061590.2233326X-RAY DIFFRACTION100
2.54-2.610.2351610.21543351X-RAY DIFFRACTION100
2.61-2.680.27341740.21433299X-RAY DIFFRACTION99.86
2.68-2.760.24841650.21833324X-RAY DIFFRACTION99.83
2.76-2.850.27941770.22163327X-RAY DIFFRACTION99.89
2.85-2.950.2211790.22463347X-RAY DIFFRACTION99.83
2.95-3.070.26941880.23533334X-RAY DIFFRACTION99.91
3.07-3.20.24051700.22043354X-RAY DIFFRACTION99.91
3.2-3.370.27461830.19823355X-RAY DIFFRACTION99.77
3.37-3.590.21791730.18393375X-RAY DIFFRACTION99.94
3.59-3.860.19631760.1763390X-RAY DIFFRACTION99.83
3.86-4.250.19141780.14633404X-RAY DIFFRACTION99.94
4.25-4.860.17861880.13843425X-RAY DIFFRACTION99.86
4.87-6.130.2072030.16363443X-RAY DIFFRACTION99.81
6.13-52.240.17911970.16613647X-RAY DIFFRACTION99.15

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