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- PDB-6y2i: Crystal structure of M. tuberculosis KasA in complex with N-(1H-i... -

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Basic information

Entry
Database: PDB / ID: 6y2i
TitleCrystal structure of M. tuberculosis KasA in complex with N-(1H-indazol-5-yl)butane-1-sulfonamide
Components3-oxoacyl-[acyl-carrier-protein] synthase 1
KeywordsTRANSFERASE / INHIBITOR / KASA / MYCOBACTERIUM TUBERCULOSIS / 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1 / ACYLTRANSFERASE / LIPID SYNTHESIS / FATTY ACID BIOSYNTHESIS
Function / homology
Function and homology information


meromycolic acid 3-oxoacyl-(acyl carrier protein) synthase I / fatty acid elongation, saturated fatty acid / fatty acid elongation / 3-oxoacyl-[acyl-carrier-protein] synthase activity / peptidoglycan-based cell wall / fatty acid biosynthetic process / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase / 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
Similarity search - Domain/homology
~{N}-(1~{H}-indazol-5-yl)butane-1-sulfonamide / 3-oxoacyl-[acyl-carrier-protein] synthase 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.533 Å
AuthorsChung, C.
CitationJournal: Acs Infect Dis. / Year: 2020
Title: Exploring the SAR of the beta-Ketoacyl-ACP Synthase Inhibitor GSK3011724A and Optimization around a Genotoxic Metabolite.
Authors: Cunningham, F. / Esquivias, J. / Fernandez-Menendez, R. / Perez, A. / Guardia, A. / Escribano, J. / Rivero, C. / Vimal, M. / Cacho, M. / de Dios-Anton, P. / Martinez-Martinez, M.S. / ...Authors: Cunningham, F. / Esquivias, J. / Fernandez-Menendez, R. / Perez, A. / Guardia, A. / Escribano, J. / Rivero, C. / Vimal, M. / Cacho, M. / de Dios-Anton, P. / Martinez-Martinez, M.S. / Jimenez, E. / Huertas Valentin, L. / Rebollo-Lopez, M.J. / Lopez-Roman, E.M. / Sousa-Morcuende, V. / Rullas, J. / Neu, M. / Chung, C.W. / Bates, R.H.
History
DepositionFeb 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: 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 1.2May 15, 2024Group: Data collection / Database references / Derived calculations
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: 3-oxoacyl-[acyl-carrier-protein] synthase 1
BBB: 3-oxoacyl-[acyl-carrier-protein] synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,36218
Polymers90,8002
Non-polymers1,56216
Water15,673870
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10000 Å2
ΔGint-12 kcal/mol
Surface area25120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.314, 75.314, 149.230
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

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Protein , 1 types, 2 molecules AAABBB

#1: Protein 3-oxoacyl-[acyl-carrier-protein] synthase 1 / Beta-ketoacyl-ACP synthase 1 / KAS 1


Mass: 45400.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: kasA, Rv2245, MTCY427.26 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WQD9, beta-ketoacyl-[acyl-carrier-protein] synthase I

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Non-polymers , 5 types, 886 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-O6Z / ~{N}-(1~{H}-indazol-5-yl)butane-1-sulfonamide


Mass: 253.321 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15N3O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 870 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.69 Å3/Da / Density % sol: 54.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 16% w/v PEG3350, 0.2M sodium citrate, 1.5mM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.917 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.8408
pseudo-merohedral22K, H, -L20.1592
ReflectionResolution: 1.53→74.61 Å / Num. obs: 141366 / % possible obs: 99.4 % / Redundancy: 4.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.8
Reflection shellResolution: 1.53→2.38 Å / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 22883 / CC1/2: 0.882

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.533→65.224 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.231 / SU ML: 0.025 / Cross valid method: FREE R-VALUE / ESU R: 0.011 / ESU R Free: 0.01
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1357 6954 4.921 %
Rwork0.1221 --
all0.123 --
obs-141302 99.422 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.026 Å2
Baniso -1Baniso -2Baniso -3
1-6.629 Å20 Å20 Å2
2--6.629 Å20 Å2
3----13.257 Å2
Refinement stepCycle: LAST / Resolution: 1.533→65.224 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6030 0 102 870 7002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0136507
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176088
X-RAY DIFFRACTIONr_angle_refined_deg1.191.6388844
X-RAY DIFFRACTIONr_angle_other_deg1.2851.58114082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1865877
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.80521.079315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.29115991
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9931553
X-RAY DIFFRACTIONr_chiral_restr0.0560.2831
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027599
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021378
X-RAY DIFFRACTIONr_nbd_refined0.1940.21197
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1690.25673
X-RAY DIFFRACTIONr_nbtor_refined0.1460.23109
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.22490
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0930.2584
X-RAY DIFFRACTIONr_metal_ion_refined0.1080.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1780.220
X-RAY DIFFRACTIONr_nbd_other0.1420.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0560.229
X-RAY DIFFRACTIONr_mcbond_it0.672.3933433
X-RAY DIFFRACTIONr_mcbond_other0.6692.3933432
X-RAY DIFFRACTIONr_mcangle_it1.1055.3884332
X-RAY DIFFRACTIONr_mcangle_other1.1055.3894333
X-RAY DIFFRACTIONr_scbond_it1.0032.6813074
X-RAY DIFFRACTIONr_scbond_other1.0032.6823075
X-RAY DIFFRACTIONr_scangle_it1.6495.884511
X-RAY DIFFRACTIONr_scangle_other1.6495.8814512
X-RAY DIFFRACTIONr_lrange_it4.32624.2757239
X-RAY DIFFRACTIONr_lrange_other3.98823.1517037
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.533-1.5720.1985170.1829913X-RAY DIFFRACTION99.0409
1.572-1.6160.1985440.1719621X-RAY DIFFRACTION99.8919
1.616-1.6620.1724510.1549529X-RAY DIFFRACTION99.8499
1.662-1.7130.165050.159177X-RAY DIFFRACTION99.835
1.713-1.770.1644670.1458878X-RAY DIFFRACTION99.8078
1.77-1.8320.1694370.148629X-RAY DIFFRACTION99.6154
1.832-1.9010.1594360.1368220X-RAY DIFFRACTION99.0049
1.901-1.9780.1453490.1298057X-RAY DIFFRACTION99.7035
1.978-2.0660.1354050.1187653X-RAY DIFFRACTION99.9628
2.066-2.1670.1333620.1167373X-RAY DIFFRACTION99.9096
2.167-2.2840.1313440.1127009X-RAY DIFFRACTION99.8235
2.284-2.4220.1183420.1126554X-RAY DIFFRACTION99.6532
2.422-2.5890.1193550.1136131X-RAY DIFFRACTION99.3414
2.589-2.7960.1363140.1175666X-RAY DIFFRACTION98.081
2.796-3.0630.1122680.115249X-RAY DIFFRACTION99.5489
3.063-3.4230.1262330.1134824X-RAY DIFFRACTION99.0597
3.423-3.9510.1212280.114151X-RAY DIFFRACTION98.5595
3.951-4.8350.1171530.1043501X-RAY DIFFRACTION97.6222
4.835-6.8190.141560.1362715X-RAY DIFFRACTION98.0198
6.819-65.2240.157880.1351498X-RAY DIFFRACTION98.5705
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)
10.0284-0.0406-0.0460.06290.07960.2859-0.0035-0.00050.00170.01020.00460.005-0.0064-0.0164-0.00110.01090.00940.0060.00880.00340.0317-26.1919.126210.5642
20.089-0.0173-0.0630.07150.02680.24280.00540.00630.0172-0.00580.0017-0.0020.03310.0575-0.00710.00860.01250.00510.030.00130.0223-7.84179.6026-11.0041
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA*4 - 416
2X-RAY DIFFRACTION2ALLB*4 - 416

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