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- PDB-7vjt: Crystal Structure of Mtb Pks13-TE in complex with inhibitor coume... -

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Basic information

Entry
Database: PDB / ID: 7vjt
TitleCrystal Structure of Mtb Pks13-TE in complex with inhibitor coumestan derivative 8
ComponentsPolyketide synthase Pks13 (Termination polyketide synthase)
KeywordsTRANSFERASE / Tuberculosis / Mycobacterium tuberculosis / ANTIBIOTIC
Function / homology
Function and homology information


secondary metabolite biosynthetic process / phosphopantetheine binding / nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
Similarity search - Function
Thioesterase / Thioesterase domain / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Chem-7IJ / Polyketide synthase Pks13 (Termination polyketide synthase)
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsZhang, W. / Wang, S.S. / Yu, L.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21778019 China
CitationJournal: J.Med.Chem. / Year: 2022
Title: Structure-Based Optimization of Coumestan Derivatives as Polyketide Synthase 13-Thioesterase(Pks13-TE) Inhibitors with Improved hERG Profiles for Mycobacterium tuberculosis Treatment.
Authors: Zhang, W. / Lun, S. / Wang, S.S. / Cai, Y.P. / Yang, F. / Tang, J. / Bishai, W.R. / Yu, L.F.
History
DepositionSep 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: 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_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 26, 2022Group: 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
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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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)65,0614
Polymers64,3302
Non-polymers7312
Water3,531196
1
A: Polyketide synthase Pks13 (Termination polyketide synthase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5312
Polymers32,1651
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)32,5312
Polymers32,1651
Non-polymers3651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.900, 38.430, 161.078
Angle α, β, γ (deg.)90.000, 101.060, 90.000
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1451 through 1607 or (resid 1608...
21(chain B and ((resid 1451 and (name N or name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNASPASP(chain A and (resid 1451 through 1607 or (resid 1608...AA1451 - 16079 - 165
12GLUGLUGLUGLU(chain A and (resid 1451 through 1607 or (resid 1608...AA1608166
21GLNGLNGLNGLN(chain B and ((resid 1451 and (name N or name...BB14519
22GLNGLNTHRTHR(chain B and ((resid 1451 and (name N or name...BB1451 - 17279 - 285
23GLNGLNTHRTHR(chain B and ((resid 1451 and (name N or name...BB1451 - 17279 - 285
24GLNGLNTHRTHR(chain B and ((resid 1451 and (name N or name...BB1451 - 17279 - 285
25GLNGLNTHRTHR(chain B and ((resid 1451 and (name N or name...BB1451 - 17279 - 285

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Components

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


Mass: 32165.135 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: pks, ERS007688_02231 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A654TNE3, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-7IJ / 3,8-bis(oxidanyl)-7-(piperidin-1-ylmethyl)-[1]benzofuro[3,2-c]chromen-6-one


Mass: 365.379 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H19NO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.05 Å3/Da / Density % sol: 40.05 %
Crystal growTemperature: 291.2 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 200 mM ammonium acetate, 100 mM sodium acetate trihydrate (pH 4.6), and 30% (w/v) polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2020
RadiationMonochromator: ADSC QUANTUM 315r / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.94→81.91 Å / Num. obs: 39267 / % possible obs: 99.3 % / Redundancy: 6 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 10.5
Reflection shellResolution: 1.94→1.98 Å / Rmerge(I) obs: 0.385 / Num. unique obs: 2481

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Processing

Software
NameVersionClassification
REFMAC7.1refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V3Y

5v3y


Resolution: 1.94→81.91 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2243 1974 5.04 %
Rwork0.185 --
obs0.187 39170 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.71 Å2 / Biso mean: 22.4313 Å2 / Biso min: 9.15 Å2
Refinement stepCycle: final / Resolution: 1.94→81.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4264 0 54 196 4514
Biso mean--15.56 25.75 -
Num. residues----550
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2544X-RAY DIFFRACTION6.61TORSIONAL
12B2544X-RAY DIFFRACTION6.61TORSIONAL
LS refinement shellResolution: 1.935→2.004 Å / R complete: 0.9648 /
RfactorNum. reflection
Rfree0.257 -
Rwork0.2037 -
obs-3780
Refinement TLS params.Method: refined / Origin x: -8.782 Å / Origin y: -24.803 Å / Origin z: 158.216 Å
111213212223313233
T0.1213 Å2-0.0011 Å2-0.0167 Å2-0.0933 Å2-0.0001 Å2--0.1444 Å2
L0.2468 °20.0055 °2-0.3577 °2-0.0255 °2-0.0105 °2--1.5961 °2
S0.0391 Å °0.0404 Å °0.0416 Å °-0.0109 Å °0.0414 Å °0.0093 Å °-0.0337 Å °-0.0314 Å °-0.0749 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1450 - 1727
2X-RAY DIFFRACTION1B1451 - 1727
3X-RAY DIFFRACTION1A1801
4X-RAY DIFFRACTION1B1801
5X-RAY DIFFRACTION1A1901 - 2003
6X-RAY DIFFRACTION1B1901 - 1993

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