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- PDB-5v41: Crystal Structure of Mtb Pks13 Thioesterase domain in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5v41
TitleCrystal Structure of Mtb Pks13 Thioesterase domain in complex with inhibitor TAM5
ComponentsPolyketide synthase Pks13 (Termination polyketide synthase)
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Thioesterase domain / TAM5 complex / Pks13 / Mycobacterium / polyketide synthase / mycolic acid condensation / TB Structural Genomics Consortium / TBSGC / alpha/beta hydrolase / thioesterase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


DIM/DIP cell wall layer assembly / biosynthetic process / hydrolase activity, acting on ester bonds / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / 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
Chem-J24 / Polyketide synthase Pks13 (Termination polyketide synthase) / Polyketide synthase Pks13
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.051 Å
AuthorsAggarwal, A. / Sacchettini, J.C.
CitationJournal: Cell / Year: 2017
Title: Development of a Novel Lead that Targets M. tuberculosis Polyketide Synthase 13.
Authors: Aggarwal, A. / Parai, M.K. / Shetty, N. / Wallis, D. / Woolhiser, L. / Hastings, C. / Dutta, N.K. / Galaviz, S. / Dhakal, R.C. / Shrestha, R. / Wakabayashi, S. / Walpole, C. / Matthews, D. / ...Authors: Aggarwal, A. / Parai, M.K. / Shetty, N. / Wallis, D. / Woolhiser, L. / Hastings, C. / Dutta, N.K. / Galaviz, S. / Dhakal, R.C. / Shrestha, R. / Wakabayashi, S. / Walpole, C. / Matthews, D. / Floyd, D. / Scullion, P. / Riley, J. / Epemolu, O. / Norval, S. / Snavely, T. / Robertson, G.T. / Rubin, E.J. / Ioerger, T.R. / Sirgel, F.A. / van der Merwe, R. / van Helden, P.D. / Keller, P. / Bottger, E.C. / Karakousis, P.C. / Lenaerts, A.J. / Sacchettini, J.C.
History
DepositionMar 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 26, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 (Termination polyketide synthase)
B: Polyketide synthase Pks13 (Termination polyketide synthase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9373
Polymers63,5552
Non-polymers3811
Water5,423301
1
A: Polyketide synthase Pks13 (Termination polyketide synthase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1592
Polymers31,7781
Non-polymers3811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polyketide synthase Pks13 (Termination polyketide synthase)


Theoretical massNumber of molelcules
Total (without water)31,7781
Polymers31,7781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.906, 109.725, 57.359
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ASPASPTHRTHRchain AAA1453 - 17276 - 280
2ILEILEARGARGchain BBB1452 - 17265 - 279

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Components

#1: Protein Polyketide synthase Pks13 (Termination polyketide synthase)


Mass: 31777.742 Da / Num. of mol.: 2 / Fragment: thioesterase domain (UNP residues 113-395)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: pks, ERS027654_02263 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0T9CRX1, UniProt: I6X8D2*PLUS, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-J24 / ethyl 5-hydroxy-4-(morpholin-4-ylmethyl)-2-phenyl-1-benzofuran-3-carboxylate


Mass: 381.422 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H23NO5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 44.12 %
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
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0075 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 33859 / % possible obs: 94.7 % / Redundancy: 5.5 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.072 / Rrim(I) all: 0.16 / Χ2: 1.547 / Net I/av σ(I): 15.07 / Net I/σ(I): 5.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)CC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.05-2.094.30.4320.6450.76298.9
2.09-2.124.80.6580.4860.71298.20.981
2.12-2.165.20.6620.4180.77899.70.8770.975
2.16-2.215.60.7680.4020.84898.80.8630.955
2.21-2.263.70.920.1882.21747.30.3240.379
2.26-2.315.30.8590.4260.912800.8920.994
2.31-2.375.80.8740.2210.95199.80.4840.534
2.37-2.435.90.9060.2060.97699.80.4540.5
2.43-2.55.90.9150.181.0561000.3970.438
2.5-2.585.90.930.1511.0941000.3330.366
2.58-2.685.90.9450.1271.1711000.2820.31
2.68-2.785.90.9580.1081.1781000.240.264
2.78-2.915.90.9660.0921.42999.90.2050.226
2.91-3.065.90.9780.0751.58899.90.1680.185
3.06-3.255.80.9810.0621.95299.90.140.153
3.25-3.515.80.9910.0522.3499.70.1170.128
3.51-3.865.20.9860.0532.83377.30.1140.126
3.86-4.425.30.9890.0443.30497.70.0960.106
4.42-5.565.50.9940.0372.86299.20.0810.09
5.56-505.40.9960.0292.324970.0620.069

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data collection
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5V3W

5v3w


Resolution: 2.051→48.199 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.11
RfactorNum. reflection% reflectionSelection details
Rfree0.2418 1702 5.06 %Random selection
Rwork0.2018 ---
obs0.2039 33653 93.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.16 Å2 / Biso mean: 39.183 Å2 / Biso min: 14.42 Å2
Refinement stepCycle: final / Resolution: 2.051→48.199 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4136 0 28 301 4465
Biso mean--40.46 43.45 -
Num. residues----544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054259
X-RAY DIFFRACTIONf_angle_d0.8825791
X-RAY DIFFRACTIONf_chiral_restr0.034626
X-RAY DIFFRACTIONf_plane_restr0.004768
X-RAY DIFFRACTIONf_dihedral_angle_d13.7641546
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2366X-RAY DIFFRACTION6.12TORSIONAL
12B2366X-RAY DIFFRACTION6.12TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.051-2.11130.34831320.27872548268091
2.1113-2.17950.28461520.24122744289699
2.1795-2.25740.3828980.35471964206270
2.2574-2.34780.33231320.24572314244682
2.3478-2.45460.25011390.220127972936100
2.4546-2.5840.27541300.21228452975100
2.584-2.74590.27771420.222628292971100
2.7459-2.95790.27541430.218728332976100
2.9579-3.25550.2551650.205928192984100
3.2555-3.72640.24991240.18252486261086
3.7264-4.69430.19241760.16072815299198
4.6943-48.21180.18781690.17532957312698
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)
11.4305-0.1286-0.57191.4546-0.34453.05110.0273-0.0635-0.02740.19390.0197-0.00510.248-0.0455-0.02280.1701-0.0043-0.02140.1582-0.01380.118118.858928.928424.5159
21.66520.2318-0.66261.25470.16480.78130.07050.01020.31280.04590.08460.1421-0.0038-0.0139-0.07560.24310.0079-0.00190.18110.00510.249410.129838.557319.0168
33.565-0.4591-0.65074.11691.38444.9399-0.05840.15960.2072-0.25250.10080.15190.03720.21470.00790.23510.0151-0.03940.2773-0.05080.3334-7.313725.70363.1395
40.974-0.4791-0.72871.26710.33490.6663-0.07480.0509-0.4162-0.2675-0.01020.28910.0286-0.02260.11280.3667-0.06310.00690.3736-0.06840.5167-8.874417.361910.371
51.5011-0.5289-0.23365.9180.89351.40190.02610.1172-0.3090.2266-0.18370.09640.1565-0.00660.140.2034-0.0278-0.03440.2334-0.03420.27293.978421.10912.371
62.50890.56661.50661.9638-1.06711.9868-0.09340.13840.3249-0.08810.00140.1675-0.1305-0.08320.0680.15120.03130.00640.20370.00070.21878.86939.885611.6979
72.4792-1.0736-0.84882.0188-0.42641.0451-0.02330.2930.0329-0.2258-0.0159-0.16790.25460.08680.05030.25250.01240.0030.24180.03630.194620.065636.45597.2401
82.83720.69441.50352.54390.87553.7964-0.15270.03570.38480.0449-0.06170.0107-0.52340.47680.23040.2025-0.0322-0.03670.19680.03320.268129.77739.99819.4557
91.5569-0.2585-0.50552.4156-0.09912.31990.00020.03380.1967-0.08390.0426-0.3202-0.06360.2169-0.03760.15780.0030.00890.1651-0.00240.220927.258466.8625.389
101.6307-0.20740.91322.15770.6732.45190.08440.1152-0.1374-0.23880.24130.44150.4887-0.5217-0.22840.3287-0.1205-0.05690.34490.08990.34847.480270.4401-14.7547
111.55660.72690.39942.918-0.05032.17180.08150.0598-0.1189-0.160.08210.07150.25950.0019-0.12540.26040.0360.01830.17760.01540.218517.975456.43467.5987
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1453 through 1548 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1549 through 1571 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1572 through 1590 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1591 through 1626 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1627 through 1644 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1645 through 1689 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 1690 through 1706 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 1707 through 1727 )A0
9X-RAY DIFFRACTION9chain 'B' and (resid 1452 through 1571 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 1572 through 1644 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 1645 through 1726 )B0

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