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- PDB-5v3w: Crystal Structure of the Apo form of Thioesterase domain of Mtb Pks13 -

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Basic information

Entry
Database: PDB / ID: 5v3w
TitleCrystal Structure of the Apo form of Thioesterase domain of Mtb Pks13
ComponentsPolyketide synthase Pks13 (Termination polyketide synthase)
KeywordsTRANSFERASE / thioesterase domain / Pks13 / Mycobacterium / polyketide synthase / mycolic acid condensation / TB Structural Genomics Consortium / TBSGC / alpha/beta hydrolase / thioesterase
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-2Q5 / Polyketide synthase Pks13 (Termination polyketide synthase) / Polyketide synthase Pks13
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.723 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)64,0564
Polymers63,5552
Non-polymers5012
Water8,485471
1
A: Polyketide synthase Pks13 (Termination polyketide synthase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0282
Polymers31,7781
Non-polymers2501
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)32,0282
Polymers31,7781
Non-polymers2501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.666, 106.913, 57.815
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 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN

Dom-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1THRTHRchain AAA1451 - 17274 - 280
2ARGARGchain 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-2Q5 / (2R)-2-{[(2R)-2-{[(2S)-2-{[(2R)-2-hydroxypropyl]oxy}propyl]oxy}propyl]oxy}propan-1-ol


Mass: 250.332 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 42.95 %
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: Dec 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. obs: 58556 / % possible obs: 99.8 % / Redundancy: 7.7 % / Biso Wilson estimate: 18.04 Å2 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.034 / Rrim(I) all: 0.096 / Χ2: 2.262 / Net I/av σ(I): 36.685 / Net I/σ(I): 10.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.72-1.756.40.5480.8490.2280.5961.15699.6
1.75-1.7870.4840.8960.1940.5221.19799.7
1.78-1.827.70.4110.9350.1560.441.30399.7
1.82-1.8580.370.9480.1380.3951.37199.8
1.85-1.8980.3560.9560.1330.381.66899.8
1.89-1.947.60.3510.9430.1360.3772.4199.8
1.94-1.9980.2480.9770.0930.2651.83999.9
1.99-2.0480.2080.980.0780.2231.89199.9
2.04-2.17.80.2070.9810.0790.2222.2599.9
2.1-2.1780.1610.9870.060.1722.104100
2.17-2.247.50.1560.9860.0610.1682.65299.9
2.24-2.337.70.1350.9890.0520.1452.397100
2.33-2.4480.1140.9930.0430.1222.365100
2.44-2.5780.1020.9940.0380.1092.478100
2.57-2.737.90.0940.9950.0360.12.772100
2.73-2.947.80.0790.9960.030.0852.86100
2.94-3.247.70.0710.9970.0270.0763.264100
3.24-3.717.30.0610.9980.0240.0663.57299.5
3.71-4.677.40.050.9980.020.0543.11199.7
4.67-507.40.0410.9980.0160.0442.37598.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å39.19 Å
Translation2.5 Å39.19 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-3000data collection
SCALEPACKdata scaling
PHASERphasing
PHENIXmodel building
PDB_EXTRACT3.15data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3TEJ

3tej


Resolution: 1.723→39.25 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.22
RfactorNum. reflection% reflectionSelection details
Rfree0.2011 2959 5.06 %Random selection
Rwork0.1692 ---
obs0.1709 58467 99.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.56 Å2 / Biso mean: 22.7052 Å2 / Biso min: 7.32 Å2
Refinement stepCycle: final / Resolution: 1.723→39.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4227 0 23 471 4721
Biso mean--29.12 30.75 -
Num. residues----547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014347
X-RAY DIFFRACTIONf_angle_d1.2495901
X-RAY DIFFRACTIONf_chiral_restr0.056636
X-RAY DIFFRACTIONf_plane_restr0.007787
X-RAY DIFFRACTIONf_dihedral_angle_d13.5991596
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2479X-RAY DIFFRACTION7.576TORSIONAL
12B2479X-RAY DIFFRACTION7.576TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7233-1.75150.2241070.1972469257692
1.7515-1.78170.24371310.187626122743100
1.7817-1.81410.23431550.17226102765100
1.8141-1.8490.21031290.166126212750100
1.849-1.88670.20151410.170826192760100
1.8867-1.92780.26451290.22142654278399
1.9278-1.97260.24031290.181925922721100
1.9726-2.02190.20111540.158726082762100
2.0219-2.07660.20681500.157526322782100
2.0766-2.13770.19011410.165526422783100
2.1377-2.20670.18471430.158926342777100
2.2067-2.28560.24391400.19242616275699
2.2856-2.37710.23181420.158826352777100
2.3771-2.48520.20381420.164526642806100
2.4852-2.61620.20421510.170926392790100
2.6162-2.78010.21941410.176626802821100
2.7801-2.99470.20771420.179326582800100
2.9947-3.29590.22061670.177326642831100
3.2959-3.77250.17831410.16012692283399
3.7725-4.75170.16211450.14227272872100
4.7517-39.26010.17671390.17872840297999
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)
11.50490.16670.44910.8278-0.00340.64910.046-0.1135-0.01440.1185-0.05020.01190.0003-0.02220.00050.114-0.00680.00730.1133-0.00210.080212.596728.416220.7124
21.5023-0.2770.0516.44383.12641.41010.1190.1091-0.13170.4254-0.3110.25250.1855-0.32240.1590.2183-0.0324-0.00050.24610.00020.1819-5.108717.483510.5855
32.69030.19020.81522.0692-0.35231.6894-0.0405-0.01140.18960.0726-0.01810.0517-0.1463-0.04840.06240.1134-0.00830.010.09590.00980.117715.772537.828113.4785
41.15520.0169-0.02851.82330.02661.67090.014-0.02730.0041-0.0577-0.001-0.0858-0.05690.1278-0.02250.0730.0007-0.00080.0974-0.00410.094227.838763.9594.7137
51.2552-0.08491.02441.3895-1.26191.96310.13090.1752-0.0828-0.4680.06850.3940.2689-0.1693-0.08070.229-0.0173-0.08470.22640.00670.25948.728667.1741-15.4144
61.18910.01140.58321.9301-0.08022.163-0.00410.0413-0.08430.09690.00920.12890.1020.0041-0.05310.0963-0.01370.01520.09710.00820.140518.184654.33747.4179
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1451 through 1590 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1591 through 1645 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1646 through 1727 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 1451 through 1571 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 1572 through 1645 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 1646 through 1726 )B0

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