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- PDB-5v3z: Crystal Structure of the D1607N mutant form of Thioesterase domai... -

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Basic information

Entry
Database: PDB / ID: 5v3z
TitleCrystal Structure of the D1607N mutant form of Thioesterase domain of Mtb Pks13
ComponentsPolyketide synthase Pks13 (Termination polyketide synthase)
KeywordsTRANSFERASE / Thioesterase domain / D1607N mutant / 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
Polyketide synthase Pks13 (Termination polyketide synthase) / Polyketide synthase Pks13
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.881 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)64,3646
Polymers63,5542
Non-polymers8114
Water6,035335
1
A: Polyketide synthase Pks13 (Termination polyketide synthase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0152
Polymers31,7771
Non-polymers2381
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)32,3494
Polymers31,7771
Non-polymers5733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.704, 108.904, 58.057
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 / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 1451 - 1726 / Label seq-ID: 4 - 279

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

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


Mass: 31776.758 Da / Num. of mol.: 2 / Fragment: thioesterase domain (UNP residues 113-395) / Mutation: D1607N
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-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.21 Å3/Da / Density % sol: 44.25 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, 2%-4% v/v PEG400, 1.8-2 M ammonium sulfate

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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: Mar 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 43322 / % possible obs: 93.2 % / Redundancy: 4.9 % / Biso Wilson estimate: 29.53 Å2 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.07 / Rrim(I) all: 0.134 / Χ2: 0.924 / Net I/av σ(I): 9.129 / Net I/σ(I): 4.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)CC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
1.88-1.912.60.2210.9760.59559.1
1.91-1.953.20.2340.920.63168.9
1.95-1.983.80.3130.7670.67475.9
1.98-2.034.30.3850.6190.68783
2.03-2.074.60.4580.5230.70187.4
2.07-2.124.70.5120.4750.71492.60.961
2.12-2.174.80.6030.3920.74596.40.7910.887
2.17-2.2350.70.3350.74999.20.6750.757
2.23-2.295.20.7350.2970.79899.60.6070.679
2.29-2.375.30.8030.2540.8221000.520.581
2.37-2.455.30.8380.2210.8061000.4540.507
2.45-2.555.30.8870.1780.8181000.3640.406
2.55-2.675.30.9270.150.8581000.3080.344
2.67-2.815.30.9430.120.8711000.2480.277
2.81-2.985.30.9740.0840.9391000.1750.195
2.98-3.215.20.9880.0571.011000.120.133
3.21-3.545.20.9940.0411.2561000.0860.096
3.54-4.055.10.9950.0341.61000.0720.08
4.05-5.150.9970.0251.4261000.0530.058
5.1-504.90.9980.0181.00299.40.0370.041

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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: 1.881→44.364 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.42
RfactorNum. reflection% reflectionSelection details
Rfree0.2297 2168 5.05 %Random selection
Rwork0.1876 ---
obs0.1897 42931 92.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.2 Å2 / Biso mean: 36.3567 Å2 / Biso min: 14.73 Å2
Refinement stepCycle: final / Resolution: 1.881→44.364 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4212 0 36 335 4583
Biso mean--48.54 41.29 -
Num. residues----550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114331
X-RAY DIFFRACTIONf_angle_d1.2545881
X-RAY DIFFRACTIONf_chiral_restr0.057636
X-RAY DIFFRACTIONf_plane_restr0.007782
X-RAY DIFFRACTIONf_dihedral_angle_d12.9741580
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2246X-RAY DIFFRACTION3.031TORSIONAL
12B2246X-RAY DIFFRACTION3.031TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8808-1.92450.3715920.3681618171056
1.9245-1.97260.3634950.31851985208069
1.9726-2.0260.30581400.29172293243380
2.026-2.08560.30371320.2622561269388
2.0856-2.15290.3181480.24022742289094
2.1529-2.22980.25751710.22292849302099
2.2298-2.31910.2611590.210228993058100
2.3191-2.42470.27841450.203229433088100
2.4247-2.55250.26931500.189928983048100
2.5525-2.71240.25091490.190629603109100
2.7124-2.92180.2531600.181929413101100
2.9218-3.21570.19431420.171829623104100
3.2157-3.68080.20511680.160829553123100
3.6808-4.63670.18551630.146130003163100
4.6367-44.37630.20381540.18363157331199
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)
13.11420.2084-0.92863.07760.15383.24050.1089-0.2884-0.09720.4303-0.0253-0.03280.15210.1325-0.09430.1857-0.005-0.04490.15450.00880.144119.032628.02724.9223
23.952-0.11941.25421.37640.18931.56730.1460.2193-0.34170.0074-0.06370.45290.2774-0.1711-0.0780.23780.01110.00990.2206-0.02150.3407-3.439325.462510.1795
33.78770.68160.28633.5408-0.35761.62830.0578-0.02040.22410.0038-0.02970.0862-0.0516-0.1423-0.02440.15580.0190.00570.1588-0.00430.146913.910435.589213.1445
41.5544-0.2599-0.22232.554-0.79082.8862-0.03440.12180.0153-0.19650.0845-0.01960.01720.1954-0.07030.1465-0.01020.00750.1511-0.00570.214522.68365.6710.1818
50.6609-0.24530.46332.7509-1.50233.1937-0.02080.0772-0.0397-0.06790.11070.26070.2147-0.0527-0.08490.1358-0.02020.01040.1835-0.0220.286915.87761.01781.2859
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1451 through 1548 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1549 through 1626 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1627 through 1726 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 1451 through 1606 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 1607 through 1726 )B0

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