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- PDB-5v42: Crystal Structure of Mtb Pks13 Thioesterase domain in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5v42
TitleCrystal Structure of Mtb Pks13 Thioesterase domain in complex with inhibitor TAM3
ComponentsPolyketide synthase Pks13 (Termination polyketide synthase)
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Thioesterase domain / TAM3 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


hydrolase activity, acting on ester bonds / biosynthetic process / nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / periplasmic space / electron transfer activity / copper ion binding
Similarity search - Function
Azurin / : / Thioesterase / Thioesterase domain / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Cupredoxin / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Chem-I66 / Polyketide synthase Pks13 (Termination polyketide synthase) / Azurin iso-2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.987 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)64,2864
Polymers63,5552
Non-polymers7312
Water4,450247
1
A: Polyketide synthase Pks13 (Termination polyketide synthase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1432
Polymers31,7781
Non-polymers3651
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)32,1432
Polymers31,7781
Non-polymers3651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.362, 109.399, 56.895
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
1GLYGLYTHRTHRchain AAA1454 - 17277 - 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-I66 / ethyl 5-hydroxy-2-phenyl-4-(pyrrolidin-1-ylmethyl)-1-benzofuran-3-carboxylate


Mass: 365.422 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H23NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.19 Å3/Da / Density % sol: 43.78 %
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: 1.0032 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: 1.0032 Å / Relative weight: 1
ReflectionResolution: 1.987→50 Å / Num. obs: 34501 / % possible obs: 88 % / Redundancy: 5.2 % / Biso Wilson estimate: 34.3 Å2 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.053 / Rrim(I) all: 0.11 / Χ2: 1.956 / Net I/av σ(I): 18.811 / Net I/σ(I): 8.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)CC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
1.99-2.024.40.4580.6331.07283.8
2.02-2.064.80.6140.5041.08389.3
2.06-2.14.90.6280.4751.16291.8
2.1-2.145.10.6360.4361.19592.60.94
2.14-2.195.20.7070.381.22392.80.8170.906
2.19-2.244.50.7290.4821.281730.989
2.24-2.34.30.7950.2641.62271.50.5260.593
2.3-2.365.50.8540.2281.43194.70.50.553
2.36-2.435.50.9090.1881.48893.80.4150.458
2.43-2.515.50.9240.1561.61193.80.3460.381
2.51-2.65.50.9510.1341.61893.40.2980.328
2.6-2.75.50.9680.1061.93193.60.2370.26
2.7-2.825.50.9730.0882.12393.50.1970.217
2.82-2.975.50.9830.0682.27592.90.1530.168
2.97-3.165.40.990.0542.56792.10.120.132
3.16-3.45.30.9930.0432.89991.20.0930.103
3.4-3.744.80.9920.0393.23862.30.0810.091
3.74-4.295.30.9960.0313.39890.20.0680.075
4.29-5.45.60.9960.0263.11588.90.0580.064
5.4-505.60.9980.0192.31186.10.0420.047

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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: 1.987→33.763 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.88
RfactorNum. reflection% reflectionSelection details
Rfree0.2333 1718 4.99 %Random selection
Rwork0.1943 ---
obs0.1963 34440 87.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.9 Å2 / Biso mean: 44.2683 Å2 / Biso min: 22.08 Å2
Refinement stepCycle: final / Resolution: 1.987→33.763 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4115 0 54 247 4416
Biso mean--37.4 46.16 -
Num. residues----538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084267
X-RAY DIFFRACTIONf_angle_d1.1195802
X-RAY DIFFRACTIONf_chiral_restr0.048618
X-RAY DIFFRACTIONf_plane_restr0.006769
X-RAY DIFFRACTIONf_dihedral_angle_d13.4551551
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2331X-RAY DIFFRACTION7.757TORSIONAL
12B2331X-RAY DIFFRACTION7.757TORSIONAL
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 (%)
1.9869-2.04530.33391470.29732511265883
2.0453-2.11130.3321360.27442842297892
2.1113-2.18680.28311530.25572822297593
2.1868-2.27430.38441090.34222081219068
2.2743-2.37780.29461600.22462892305294
2.3778-2.50310.29611500.20342881303194
2.5031-2.65990.22691430.20272887303094
2.6599-2.86520.27871310.20372917304893
2.8652-3.15330.24621660.20032853301992
3.1533-3.60910.23961440.17322687283188
3.6091-4.54540.16631370.15482459259684
4.5454-33.76820.1821420.16872890303287
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)
11.32050.1854-0.36731.3161-0.33152.61220.0178-0.1065-0.07140.09770.05950.05860.143-0.0625-0.06050.30740.0115-0.01030.26670.00830.265118.787929.198124.5643
20.85030.3993-0.91731.1371-0.4941.37360.09520.09480.1581-0.0160.18330.22-0.06740.003-0.13260.29180.02030.02680.28040.00130.35199.981238.525117.948
31.9064-0.1279-0.27142.96331.59033.7034-0.16620.3619-0.0629-0.278-0.13720.2901-0.31550.3070.08070.3791-0.0103-0.04830.4202-0.00270.4838-7.339325.59273.4288
42.38270.30070.55221.66060.12430.89880.07850.0856-0.23720.0373-0.07670.12480.1592-0.15150.00140.3479-0.01490.01510.3592-0.01840.311.230926.143512.375
52.3660.90041.47792.0818-0.67512.43250.06640.20240.1429-0.0848-0.04130.1504-0.0958-0.3549-0.04490.22250.02940.02560.3240.040.29716.589339.67348.8943
61.998-0.363-0.19291.4765-1.00310.8093-0.03190.17480.3419-0.0019-0.1033-0.2326-0.06320.27160.09790.2908-0.00980.01250.28910.02290.312625.465238.500614.0591
71.8791-0.01560.03992.58140.50442.15160.02520.08460.1852-0.09610.0399-0.4367-0.04070.1191-0.03710.279200.02220.26470.01290.345526.957966.61774.8092
81.41120.12721.37722.67580.27791.3211-0.1923-0.1133-0.0257-0.38250.43170.3276-0.0373-0.253-0.11250.418-0.0965-0.03080.47480.10460.40145.247370.0025-17.2452
90.84280.06240.60911.7559-1.20421.943-0.0440.1609-0.0869-0.14170.14050.03740.22730.0376-0.07820.3317-0.02930.01410.3056-0.01430.376115.481759.0789-1.8592
100.96280.2357-0.47182.10270.42971.4278-0.1004-0.230.13260.52180.079-0.07090.124-0.03470.00140.37710.0237-0.01920.30310.02630.323119.77359.214515.5796
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1454 through 1549 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1550 through 1571 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1572 through 1590 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1591 through 1664 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1665 through 1689 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1690 through 1727 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 1451 through 1571 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 1572 through 1626 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 1627 through 1689 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 1690 through 1726 )B0

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