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- PDB-9c1v: M. tuberculosis PKS13 acyltransferase (AT) domain in complex with... -

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Basic information

Entry
Database: PDB / ID: 9c1v
TitleM. tuberculosis PKS13 acyltransferase (AT) domain in complex with SuFEx inhibitor CMX410
ComponentsPolyketide synthase Pks13
KeywordsTRANSFERASE/TRANSFERSE INHIBITOR / polyketide synthase / acyltransferase / tuberculosis / inhibitor / Structural Genomics / TB Structural Genomics Consortium / TBSGC / TRANSFERASE / TRANSFERASE-TRANSFERSE INHIBITOR complex
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: 2.57 Å
AuthorsKrieger, I.K. / Tang, S. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
Funding support United States, 3items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-040487 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI095208 United States
Welch FoundationA-0015 United States
CitationJournal: To Be Published
Title: A SuFEx-based TB clinical candidate irreversibly inhibits Pks13
Authors: Krieger, I.K. / Sacchettini, J.C. / McNamara, C.W.
History
DepositionMay 29, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)115,45321
Polymers111,0932
Non-polymers4,36019
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.531, 106.531, 259.042
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
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
11A-1289-

HOH

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Components

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Protein / Sugars , 2 types, 9 molecules AB

#1: 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
#2: 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, 240 molecules

#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-A1ATW / N-(1-{3,5-difluoro-4-[(4-{[fluorodi(hydroxy)-lambda~4~-sulfanyl]oxy}phenoxy)methyl]phenyl}-1H-1,2,4-triazol-3-yl)methanesulfonamide


Mass: 480.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15F3N4O6S2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.31 Å3/Da / Density % sol: 62.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH7.5, 1.8 M AmSO4, 4-6% PEG400

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 2.57→49.26 Å / Num. obs: 48517 / % possible obs: 100 % / Redundancy: 9.3 % / Biso Wilson estimate: 51.49 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.322 / Rpim(I) all: 0.131 / Net I/σ(I): 9.3
Reflection shellResolution: 2.57→2.65 Å / Rmerge(I) obs: 3.369 / Num. unique obs: 4391 / CC1/2: 0.353

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.57→49.26 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2382 2396 4.95 %
Rwork0.1937 --
obs0.1959 48408 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.57→49.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7110 0 270 228 7608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d1.102
X-RAY DIFFRACTIONf_dihedral_angle_d12.8141048
X-RAY DIFFRACTIONf_chiral_restr0.0521191
X-RAY DIFFRACTIONf_plane_restr0.0111298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.57-2.620.42091350.33312643X-RAY DIFFRACTION100
2.62-2.680.33011280.32022663X-RAY DIFFRACTION100
2.68-2.740.35581630.30292663X-RAY DIFFRACTION100
2.74-2.810.35371510.28942632X-RAY DIFFRACTION100
2.81-2.890.28461430.27252649X-RAY DIFFRACTION100
2.89-2.970.29461360.26222680X-RAY DIFFRACTION100
2.97-3.070.31931330.23232659X-RAY DIFFRACTION100
3.07-3.180.26941300.23532690X-RAY DIFFRACTION100
3.18-3.30.23661390.20792671X-RAY DIFFRACTION100
3.3-3.450.27551250.2082727X-RAY DIFFRACTION100
3.45-3.640.27051380.19892668X-RAY DIFFRACTION100
3.64-3.860.25041200.17952741X-RAY DIFFRACTION100
3.86-4.160.21041450.15612700X-RAY DIFFRACTION100
4.16-4.580.19831440.1482735X-RAY DIFFRACTION100
4.58-5.240.18441580.14452736X-RAY DIFFRACTION100
5.24-6.60.1971450.17392802X-RAY DIFFRACTION100
6.6-49.260.18771630.16252953X-RAY DIFFRACTION100

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