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- PDB-5v40: Crystal Structure of Mtb Pks13 Thioesterase domain in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5v40
TitleCrystal Structure of Mtb Pks13 Thioesterase domain in complex with inhibitor TAM6
ComponentsPolyketide synthase Pks13 (Termination polyketide synthase)
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Thioesterase domain / TAM6 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 / fatty acid synthase activity / hydrolase activity, acting on ester bonds / biosynthetic process / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / nucleotidyltransferase activity / fatty acid biosynthetic process / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / 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 domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase ...Thioesterase / Thioesterase domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / 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-JS1 / Polyketide synthase Pks13 (Termination polyketide synthase) / Polyketide synthase Pks13
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.991 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)64,2344
Polymers63,5552
Non-polymers6792
Water7,170398
1
A: Polyketide synthase Pks13 (Termination polyketide synthase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1172
Polymers31,7781
Non-polymers3391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polyketide synthase Pks13 (Termination polyketide synthase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1172
Polymers31,7781
Non-polymers3391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.017, 109.364, 57.029
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
1ILEILETHRTHRchain AAA1452 - 17275 - 280
2GLNGLNARGARGchain BBB1451 - 17264 - 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-JS1 / ethyl 4-[(dimethylamino)methyl]-5-hydroxy-2-phenyl-1-benzofuran-3-carboxylate


Mass: 339.385 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H21NO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.16 Å3/Da / Density % sol: 43.04 %
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: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 10, 2013
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 38140 / % possible obs: 99 % / Redundancy: 4.3 % / Biso Wilson estimate: 26.51 Å2 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.065 / Rrim(I) all: 0.13 / Χ2: 1.111 / Net I/σ(I): 5.8 / Num. measured all: 162797
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
1.99-2.02417220.5780.5340.90590.7
2.02-2.064.218140.6270.4550.96996.70.895
2.06-2.14.218830.6890.3970.95398.60.7770.877
2.1-2.144.318690.7720.3390.96299.30.6580.744
2.14-2.194.319130.8520.2870.99399.80.5560.629
2.19-2.244.318730.8410.2620.9991000.5050.572
2.24-2.34.319220.8910.2321.03999.90.4480.507
2.3-2.364.318960.9120.1881.0381000.3630.411
2.36-2.434.319040.8940.1881.0311000.360.409
2.43-2.514.319190.930.1551.0241000.2980.338
2.51-2.64.319090.9360.1471.05299.90.2830.32
2.6-2.74.319140.9490.1191.1571000.2290.26
2.7-2.824.319190.9660.1021.1271000.1950.222
2.82-2.974.319150.980.0781.21899.90.1510.171
2.97-3.164.319330.9880.0561.16699.80.1070.122
3.16-3.44.319150.9940.0391.19999.70.0740.084
3.4-3.744.319480.9940.0361.6199.70.070.079
3.74-4.294.319440.9960.0281.63199.30.0550.062
4.29-5.44.319720.9980.021.13398.80.0390.044
5.4-504.120560.9990.0180.94497.40.0320.037

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
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: 1.991→46.448 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1909 5.01 %Random selection
Rwork0.1848 36172 --
obs0.1865 38081 98.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.78 Å2 / Biso mean: 33.746 Å2 / Biso min: 14 Å2
Refinement stepCycle: final / Resolution: 1.991→46.448 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4188 0 50 398 4636
Biso mean--28.72 38.4 -
Num. residues----548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064335
X-RAY DIFFRACTIONf_angle_d0.8635898
X-RAY DIFFRACTIONf_chiral_restr0.053632
X-RAY DIFFRACTIONf_plane_restr0.007784
X-RAY DIFFRACTIONf_dihedral_angle_d11.8862554
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2504X-RAY DIFFRACTION7.716TORSIONAL
12B2504X-RAY DIFFRACTION7.716TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9909-2.04070.30431270.28832370249793
2.0407-2.09590.32551470.2592527267498
2.0959-2.15760.26661230.24162535265899
2.1576-2.22720.30331370.225325842721100
2.2272-2.30680.25081420.209225522694100
2.3068-2.39920.26551320.200425882720100
2.3992-2.50840.26281320.196326102742100
2.5084-2.64060.25891370.19925682705100
2.6406-2.8060.25361480.206425982746100
2.806-3.02260.28141290.194126162745100
3.0226-3.32670.1771550.177725962751100
3.3267-3.80790.18991370.1542625276299
3.8079-4.79680.16221260.13922662278899
4.7968-46.46060.16021370.17632741287898
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)
11.3995-0.02330.18811.37610.0752.14320.0995-0.1382-0.13290.2995-0.01720.00490.2067-0.0427-0.06960.1998-0.0169-0.02950.1430.01590.104919.060228.811824.3889
22.40080.21880.71740.69230.060.90630.0390.0398-0.11760.0254-0.02960.1840.0499-0.0963-0.00180.1370.01480.02090.1515-0.01150.16491.953830.030911.421
32.176-0.2540.09641.4741-0.88190.544-0.00010.13110.15950.0835-0.0159-0.2849-0.12590.1760.05940.1893-0.0053-0.00380.20270.01230.201525.451838.435213.7747
41.8256-0.2298-0.82052.5249-0.16831.9927-0.0437-0.03010.15690.01150.1282-0.31390.04050.1425-0.06230.13780.0172-0.02880.1441-0.00190.203127.089666.98035.3223
51.09960.97710.42811.428-0.56271.55140.0587-0.1083-0.14650.25890.44750.2191-0.063-0.5-0.15820.5231-0.1087-0.11470.50160.09550.40823.036563.1396-14.5764
61.06660.05170.24681.45740.11121.5011-0.01550.1533-0.0105-0.34780.17680.38130.1986-0.3301-0.13430.2643-0.0971-0.09410.28150.050.29398.061872.4283-14.2321
71.10180.0088-0.23262.3613-0.35231.9296-0.04850.0398-0.11140.05760.09810.08820.37970.0096-0.02850.23410.01580.00090.16280.01260.18817.969356.32687.19
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1452 through 1548 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1549 through 1689 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1690 through 1727 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 1451 through 1571 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 1572 through 1588 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 1589 through 1644 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 1645 through 1726 )B0

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