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- PDB-8tr4: Crystal Structure of Mtb Pks13 Thioesterase domain in complex wit... -

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Basic information

Entry
Database: PDB / ID: 8tr4
TitleCrystal Structure of Mtb Pks13 Thioesterase domain in complex with inhibitor X20404
ComponentsPolyketide synthase Pks13
KeywordsBIOSYNTHETIC PROTEIN / polyketide synthase / thioesterase
Function / homology
Function and homology information


periplasmic space / electron transfer activity / copper ion binding
Similarity search - Function
Azurin / : / 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
Similarity search - Domain/homology
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKrieger, I.V. / Sacchettini, J.C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI095208 United States
Welch FoundationA-0015 United States
Bill & Melinda Gates FoundationINV-040487 United States
CitationJournal: Acs Infect Dis. / Year: 2024
Title: Inhibitors of the Thioesterase Activity of Mycobacterium tuberculosis Pks13 Discovered Using DNA-Encoded Chemical Library Screening.
Authors: Krieger, I.V. / Yalamanchili, S. / Dickson, P. / Engelhart, C.A. / Zimmerman, M.D. / Wood, J. / Clary, E. / Nguyen, J. / Thornton, N. / Centrella, P.A. / Chan, B. / Cuozzo, J.W. / ...Authors: Krieger, I.V. / Yalamanchili, S. / Dickson, P. / Engelhart, C.A. / Zimmerman, M.D. / Wood, J. / Clary, E. / Nguyen, J. / Thornton, N. / Centrella, P.A. / Chan, B. / Cuozzo, J.W. / Gengenbacher, M. / Guie, M.A. / Guilinger, J.P. / Bienstock, C. / Hartl, H. / Hupp, C.D. / Jetson, R. / Satoh, T. / Yeoman, J.T.S. / Zhang, Y. / Dartois, V. / Schnappinger, D. / Keefe, A.D. / Sacchettini, J.C.
History
DepositionAug 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyketide synthase Pks13
B: Polyketide synthase Pks13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,04710
Polymers63,5552
Non-polymers1,4918
Water4,900272
1
A: Polyketide synthase Pks13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6206
Polymers31,7781
Non-polymers8425
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polyketide synthase Pks13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4274
Polymers31,7781
Non-polymers6503
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.942, 87.592, 109.382
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11B-1802-

SO4

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Components

#1: Protein Polyketide synthase Pks13 / Termination polyketide synthase


Mass: 31777.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: pks13, Rv3800c / Production host: Escherichia coli (E. coli)
References: UniProt: I6X8D2, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-K6C / 4-(2-{(4M)-4-[(6M)-6-(2,5-dimethoxyphenyl)pyridin-3-yl]-1H-1,2,3-triazol-1-yl}ethyl)-N,N-dimethylbenzamide


Mass: 457.524 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H27N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 43.67 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging 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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.1→48.37 Å / Num. obs: 30403 / % possible obs: 92.1 % / Redundancy: 3.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.052 / Net I/σ(I): 10.1
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1817 / CC1/2: 0.633 / Rpim(I) all: 0.54 / % possible all: 68

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Processing

Software
NameClassification
PDB-REDOrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→48.37 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.928 / SU B: 11.056 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.276 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23764 1511 5 %RANDOM
Rwork0.18454 ---
obs0.18711 28866 91.4 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.196 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å2-0 Å2
2---0.39 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4294 0 98 272 4664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0164514
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164062
X-RAY DIFFRACTIONr_angle_refined_deg1.0921.8186135
X-RAY DIFFRACTIONr_angle_other_deg0.41.5759446
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7835.363593
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03310715
X-RAY DIFFRACTIONr_chiral_restr0.0530.2644
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025261
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02913
X-RAY DIFFRACTIONr_mcbond_it2.062.0522188
X-RAY DIFFRACTIONr_mcbond_other2.0582.0512188
X-RAY DIFFRACTIONr_mcangle_it3.1883.0622730
X-RAY DIFFRACTIONr_mcangle_other3.1893.0632731
X-RAY DIFFRACTIONr_scbond_it2.8462.3922326
X-RAY DIFFRACTIONr_scbond_other2.5462.3322302
X-RAY DIFFRACTIONr_scangle_other3.9333.4063366
X-RAY DIFFRACTIONr_long_range_B_refined6.72529.2825167
X-RAY DIFFRACTIONr_long_range_B_other6.6828.5015115
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 76 -
Rwork0.276 1544 -
obs--67.36 %
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)
11.2375-0.44690.11912.2406-0.40911.3256-0.04-0.06540.05870.06790.07240.0597-0.07240.02-0.03240.026-0.0134-0.00140.12130.0020.036616.82932.44224.1
22.2824-0.21360.2031.15550.19352.4871-0.0787-0.0893-0.067-0.0003-0.02180.0517-0.0461-0.08140.10050.0482-0.02480.00810.0672-0.00860.0420.73324.214-9.792
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1451 - 1727
2X-RAY DIFFRACTION2B1451 - 1726

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