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- PDB-5v3y: Crystal Structure of Mtb Pks13 Thioesterase domain in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5v3y
TitleCrystal Structure of Mtb Pks13 Thioesterase domain in complex with inhibitor TAM16
ComponentsPolyketide synthase Pks13 (Termination polyketide synthase)
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Thioesterase domain / TAM16 complex / Pks13 / Mycobacterium / polyketide synthase / mycolic acid condensation / TB Structural Genomics Consortium / TBSGC / alpha/beta hydrolase / THIOESTERASE-TRANSFERASE INHIBITOR complex / 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 / nucleotidyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / 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-5V8 / Polyketide synthase Pks13 (Termination polyketide synthase) / Polyketide synthase Pks13
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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)64,4125
Polymers63,5552
Non-polymers8573
Water5,567309
1
A: Polyketide synthase Pks13 (Termination polyketide synthase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1582
Polymers31,7781
Non-polymers3801
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)32,2543
Polymers31,7781
Non-polymers4772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.627, 108.762, 56.735
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
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-5V8 / 2-(4-hydroxyphenyl)-~{N}-methyl-5-oxidanyl-4-(piperidin-1-ylmethyl)-1-benzofuran-3-carboxamide


Mass: 380.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H24N2O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.18 Å3/Da / Density % sol: 43.46 %
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: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 41704 / % possible obs: 94.1 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.072 / Rrim(I) all: 0.15 / Χ2: 1.924 / Net I/av σ(I): 20.506 / Net I/σ(I): 5.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
1.9-1.9340.9070.7820.5013.27386.5
1.93-1.976.30.3730.75999.9
1.97-2.017.10.5670.7130.82100
2.01-2.057.20.6580.5290.884100
2.05-2.097.30.7410.4540.954100
2.09-2.147.30.9280.7650.3691.0371001
2.14-2.197.30.820.8380.3271.111000.884
2.19-2.254.90.3670.9590.191.92349.70.418
2.25-2.326.80.7240.8840.2991.39279.50.785
2.32-2.397.30.4450.9270.1791.4191000.48
2.39-2.487.20.3820.930.1541.5151000.413
2.48-2.587.20.320.9520.1291.6631000.345
2.58-2.77.20.260.9660.1051.8971000.281
2.7-2.847.10.2190.9730.0892.15599.90.237
2.84-3.0270.1740.9820.0722.4591000.189
3.02-3.256.80.1360.9870.0582.95699.90.148
3.25-3.586.60.1130.9910.0493.45199.60.123
3.58-4.095.60.0940.9890.0443.98267.10.104
4.09-5.166.40.0770.9940.0343.61999.90.084
5.16-506.30.0660.9960.0293.18299.20.072

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Processing

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

5v3w


Resolution: 1.98→34.584 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.36
RfactorNum. reflection% reflectionSelection details
Rfree0.2386 1861 5.07 %Random selection
Rwork0.1936 ---
obs0.1959 36725 93.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.42 Å2 / Biso mean: 36.5317 Å2 / Biso min: 11.9 Å2
Refinement stepCycle: final / Resolution: 1.98→34.584 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4155 0 61 309 4525
Biso mean--30.96 40.35 -
Num. residues----542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074306
X-RAY DIFFRACTIONf_angle_d1.0855863
X-RAY DIFFRACTIONf_chiral_restr0.071626
X-RAY DIFFRACTIONf_plane_restr0.006776
X-RAY DIFFRACTIONf_dihedral_angle_d12.4991556
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2128X-RAY DIFFRACTION6.349TORSIONAL
12B2128X-RAY DIFFRACTION6.349TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.98-2.03350.31811460.250228372983100
2.0335-2.09340.39851510.31852783293499
2.0934-2.16090.30411630.239728192982100
2.1609-2.23810.32381140.23772015212972
2.2381-2.32770.279970.27131917201468
2.3277-2.43360.22941520.200828513003100
2.4336-2.56190.21641440.189228633007100
2.5619-2.72240.21951640.187428623026100
2.7224-2.93250.25861380.196728592997100
2.9325-3.22740.24961710.187228723043100
3.2274-3.69390.23211260.17832486261287
3.6939-4.65220.18051460.16262622276893
4.6522-34.58910.23811490.187930783227100
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)
13.06380.11870.31722.4809-0.38123.32480.0215-0.3347-0.08510.24610.04670.11460.1597-0.1092-0.04070.15810.0090.00130.15740.00530.124917.324130.640623.4371
27.9088-1.7812-3.68824.44463.41598.95860.03560.1557-0.03440.16890.3613-0.64380.02970.5438-0.34170.2632-0.0064-0.05870.2861-0.02010.4426-7.113225.23312.5811
37.469-1.991.20452.72490.37044.02430.2174-0.9148-0.4495-0.807-0.08510.25940.2584-0.3868-0.05950.5649-0.17730.00980.437-0.00970.4084-9.039918.03579.0886
44.01821.26810.92814.62040.25713.6206-0.02730.13790.0439-0.1694-0.03430.2452-0.0081-0.33410.05360.12920.03340.00710.20670.01780.15097.74934.232311.9028
55.59030.34081.57223.9288-0.45735.1521-0.01770.11220.33960.1406-0.0464-0.2325-0.10580.439-0.07050.1311-0.01230.04370.14880.03340.219525.479238.278813.9092
62.5288-0.3662-0.15183.84610.03413.1953-0.09290.03360.35730.01010.1508-0.8044-0.15930.4182-0.02250.1853-0.009-0.01010.1771-0.02620.40727.115266.38774.68
71.0628-0.69290.54133.2925-2.00483.3086-0.07390.0717-0.0462-0.16550.22330.16250.2979-0.2304-0.16350.2056-0.0640.02390.2219-0.01350.247812.938862.3659-2.9454
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1453 through 1571 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1572 through 1590 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1591 through 1626 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1627 through 1689 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1690 through 1727 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 1451 through 1571 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 1572 through 1726 )B0

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