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- PDB-7m7v: Crystal Structure of Mtb Pks13 Thioesterase domain in complex wit... -

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Basic information

Entry
Database: PDB / ID: 7m7v
TitleCrystal Structure of Mtb Pks13 Thioesterase domain in complex with Compound 6
ComponentsPolyketide synthase Pks13
KeywordsTRANSFERASE/INHIBITOR / Thioesterase domain / Compound 6 complex / Pks13 / Mycobacterium / polyketide synthase / mycolic acid condensation / alpha/beta hydrolase / thioesterase / TRANSFERASE-TRANSFERASE INHIBITOR complex / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


DIM/DIP cell wall layer assembly / fatty acid synthase activity / secondary metabolite biosynthetic process / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / fatty acid biosynthetic process / plasma membrane / cytoplasm
Similarity search - Function
Thioesterase / Thioesterase domain / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase ...Thioesterase / Thioesterase domain / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / 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
Chem-Z3J / Polyketide synthase Pks13
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsAggarwal, A. / Sacchettini, J.C.
CitationJournal: J.Med.Chem. / Year: 2022
Title: Optimization of TAM16, a Benzofuran That Inhibits the Thioesterase Activity of Pks13; Evaluation toward a Preclinical Candidate for a Novel Antituberculosis Clinical Target.
Authors: Wilson, C. / Ray, P. / Zuccotto, F. / Hernandez, J. / Aggarwal, A. / Mackenzie, C. / Caldwell, N. / Taylor, M. / Huggett, M. / Mathieson, M. / Murugesan, D. / Smith, A. / Davis, S. / Cocco, ...Authors: Wilson, C. / Ray, P. / Zuccotto, F. / Hernandez, J. / Aggarwal, A. / Mackenzie, C. / Caldwell, N. / Taylor, M. / Huggett, M. / Mathieson, M. / Murugesan, D. / Smith, A. / Davis, S. / Cocco, M. / Parai, M.K. / Acharya, A. / Tamaki, F. / Scullion, P. / Epemolu, O. / Riley, J. / Stojanovski, L. / Lopez-Roman, E.M. / Torres-Gomez, P.A. / Toledo, A.M. / Guijarro-Lopez, L. / Camino, I. / Engelhart, C.A. / Schnappinger, D. / Massoudi, L.M. / Lenaerts, A. / Robertson, G.T. / Walpole, C. / Matthews, D. / Floyd, D. / Sacchettini, J.C. / Read, K.D. / Encinas, L. / Bates, R.H. / Green, S.R. / Wyatt, P.G.
History
DepositionMar 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)64,3724
Polymers63,5552
Non-polymers8172
Water1,72996
1
A: Polyketide synthase Pks13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1862
Polymers31,7781
Non-polymers4081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polyketide synthase Pks13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1862
Polymers31,7781
Non-polymers4081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.970, 110.280, 57.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYLYSLYS(chain 'A' and (resid 1454 through 1507 or (resid 1508...AA1454 - 15887 - 141
12PROPROGLNGLN(chain 'A' and (resid 1454 through 1507 or (resid 1508...AA1595 - 1620148 - 173
13ILEILEARGARG(chain 'A' and (resid 1454 through 1507 or (resid 1508...AA1625 - 1726178 - 279
21GLYGLYLYSLYS(chain 'B' and (resid 1454 through 1503 or (resid 1504...BB1454 - 15887 - 141
22PROPROGLNGLN(chain 'B' and (resid 1454 through 1503 or (resid 1504...BB1595 - 1620148 - 173
23ILEILEARGARG(chain 'B' and (resid 1454 through 1503 or (resid 1504...BB1625 - 1726178 - 279

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Components

#1: Protein Polyketide synthase Pks13 / Termination polyketide synthase


Mass: 31777.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: pks13, Rv3800c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: I6X8D2, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-Z3J / 5-hydroxy-2-(4-hydroxyphenyl)-N-methyl-4-[(2-oxa-6-azaspiro[3.4]octan-6-yl)methyl]-1-benzofuran-3-carboxamide


Mass: 408.447 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H24N2O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.27 Å3/Da / Density % sol: 45.84 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting 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: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.29→48.53 Å / Num. obs: 26061 / % possible obs: 97.73 % / Redundancy: 6.2 % / Biso Wilson estimate: 45.2 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.1514 / Rpim(I) all: 0.06725 / Net I/σ(I): 9.6
Reflection shellResolution: 2.29→2.372 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.738 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2545 / CC1/2: 0.443 / CC star: 0.783 / % possible all: 98.15

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5V3W

5v3w


Resolution: 2.29→48.53 Å / SU ML: 0.3433 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.4227
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2689 1304 5.03 %
Rwork0.2226 24605 -
obs0.2249 25909 97.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.23 Å2
Refinement stepCycle: LAST / Resolution: 2.29→48.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4035 0 60 96 4191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00874196
X-RAY DIFFRACTIONf_angle_d0.94245721
X-RAY DIFFRACTIONf_chiral_restr0.0574614
X-RAY DIFFRACTIONf_plane_restr0.0074753
X-RAY DIFFRACTIONf_dihedral_angle_d14.0097618
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.380.36451400.30882697X-RAY DIFFRACTION98.34
2.38-2.490.39911490.31922729X-RAY DIFFRACTION99.45
2.49-2.620.40911410.30932748X-RAY DIFFRACTION99.86
2.62-2.790.33521600.28222740X-RAY DIFFRACTION99.76
2.79-30.32041600.25532761X-RAY DIFFRACTION99.69
3-3.30.29571450.23672772X-RAY DIFFRACTION99.73
3.3-3.780.27151340.22562659X-RAY DIFFRACTION94.52
3.78-4.760.21881240.16982552X-RAY DIFFRACTION89.32
4.76-48.530.19781510.19082947X-RAY DIFFRACTION99.2
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)
11.809726478190.007685616370420.6167560930450.731548983520.2522994829561.409732671730.0351941096891-0.1589194536220.008963931669780.1337978379490.009760529843280.1549672591270.0415832395672-0.0710716560163-0.0001829790644640.404748177564-0.0380550038967-0.007640939783140.3606944173830.01927534614540.38378315757513.591439268430.177593846620.3666872438
20.5200532417440.000179781644629-0.0008564662229050.0282957184032-0.06955557326580.183122265633-0.0244333065832-0.635218680695-0.532588056903-0.7121542132850.3710650394140.425416909423-0.2245342948420.1127670889820.03779277780480.580165565469-0.0822928532197-0.02627025028060.755479207183-0.04419966915980.458001091179-9.4545839144718.327970295710.9513027844
33.22381077881-0.1961766531230.3168363203712.06477826376-0.5640354633381.51420035441-0.05320692568360.1597161935660.160935743106-0.1774191163910.03408045150510.1531395347640.02270597709450.0130043540355-0.0001969223273490.360027849257-0.00782538906438-0.01166116282960.3604383659040.01336959040360.28917456462714.053450953536.214058012212.596048895
41.21135708626-0.409283217403-1.221669844430.998240622642-0.07675472087331.41943757364-0.186932380144-0.2005326890570.5234467262640.4158092796680.2548394154430.0611129603071-0.3854407175270.09535500840190.0004322789524470.4727192955490.00719663121441-0.08588027903660.4298464067970.01453854773940.5378123117325.659505054172.575147432711.5070938863
50.778049677390.053097488302-0.5679535902520.496148627138-0.1455585738170.5957572599080.4022380537650.07641727060390.600213434080.252909205522-0.288948591523-0.364569953886-0.497660539950.795263949505-0.004279789912370.53422644056-0.004279647071120.001913041616050.5462847721580.09301504196090.562367592226.497659401771.7530966367.86325130004
60.9253095866120.08235870492530.339452549711.88514304658-1.068360093182.24507400095-0.1001512122230.135625880451-0.000535495383381-0.2099871886090.0417701686985-0.03787364965230.23790196357-0.1032437948290.000586910824590.423527209792-0.03635880757530.01157495956420.413662450216-0.00983678606840.48908676237917.668639470567.0922841607-6.72697506808
70.1611635608-0.192074892472-0.0966975180470.661362220604-0.5078792837220.8219161061690.296202270090.04090159224790.355269228913-0.3672356759330.05853149515820.02748364951460.148086001239-0.113952241523-8.78302279277E-50.5655691564710.0378627081238-0.01047791835830.474534297470.006710663306320.56416095685820.704062198255.43427569773.44415197255
82.245637253270.2583010549970.1570371997160.376761640596-0.1243905020611.227058332080.04667166915350.94260810536-1.3823363311-0.6777588981890.1365423259340.136141949070.2873222301650.4863552468070.001769911179690.640899735033-0.072032920386-0.01946028682220.45536527120.01004021814080.55096364896414.394431261353.0620239835-1.29918271913
90.9417112015180.557337024686-1.045384190351.571414098730.06208819785641.4852223959-0.0470958783606-0.1976542164840.1124870211160.763868725318-0.06205602503820.3593639637970.2982045129490.0465928321502-0.004151599796230.5341214381550.0411895394488-0.004759889858910.395865428505-0.001333105752280.40464998577919.832874624559.413064035115.9146394742
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1454 through 1590 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1591 through 1626 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1627 through 1726 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1452 through 1490 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1491 through 1506 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1507 through 1644 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1645 through 1664 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1665 through 1689 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1690 through 1726 )

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