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- PDB-6p9l: Crystal structure of Mycobacterium tuberculosis KasA in complex w... -

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Basic information

Entry
Database: PDB / ID: 6p9l
TitleCrystal structure of Mycobacterium tuberculosis KasA in complex with JFX
Components3-oxoacyl-[acyl-carrier-protein] synthase 1
KeywordsTRANSFERASE / BETA KETOACYL SYNTHASE I / 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 / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain ...Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Chem-JFX / 3-oxoacyl-[acyl-carrier-protein] synthase 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.305 Å
AuthorsCapodagli, G.C. / Neiditch, M.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI109713 United States
CitationJournal: Cell Chem Biol / Year: 2020
Title: A Preclinical Candidate Targeting Mycobacterium tuberculosis KasA.
Authors: Inoyama, D. / Awasthi, D. / Capodagli, G.C. / Tsotetsi, K. / Sukheja, P. / Zimmerman, M. / Li, S.G. / Jadhav, R. / Russo, R. / Wang, X. / Grady, C. / Richmann, T. / Shrestha, R. / Li, L. / ...Authors: Inoyama, D. / Awasthi, D. / Capodagli, G.C. / Tsotetsi, K. / Sukheja, P. / Zimmerman, M. / Li, S.G. / Jadhav, R. / Russo, R. / Wang, X. / Grady, C. / Richmann, T. / Shrestha, R. / Li, L. / Ahn, Y.M. / Ho Liang, H.P. / Mina, M. / Park, S. / Perlin, D.S. / Connell, N. / Dartois, V. / Alland, D. / Neiditch, M.B. / Kumar, P. / Freundlich, J.S.
History
DepositionJun 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 11, 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
Item: _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
A: 3-oxoacyl-[acyl-carrier-protein] synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8439
Polymers43,1421
Non-polymers7018
Water1,38777
1
A: 3-oxoacyl-[acyl-carrier-protein] synthase 1
hetero molecules

A: 3-oxoacyl-[acyl-carrier-protein] synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,68518
Polymers86,2832
Non-polymers1,40216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area8020 Å2
ΔGint-32 kcal/mol
Surface area26620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.804, 77.804, 146.374
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-651-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 43141.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: kasA, Rv2245, MTCY427.26
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: P9WQD9, beta-ketoacyl-[acyl-carrier-protein] synthase I

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Non-polymers , 5 types, 85 molecules

#2: Chemical ChemComp-JFX / 4-fluoro-N-(3-methyl-1H-indazol-5-yl)butane-1-sulfonamide


Mass: 285.338 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16FN3O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.96 Å3/Da / Density % sol: 58.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 200mM NaCl, 6% Isopropanol, 1mM tris(2-carboxyethyl)phosphone hydrochloride (TCEP HCl)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 17, 2018
RadiationMonochromator: 0.97946 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 23296 / % possible obs: 99.9 % / Redundancy: 9.5 % / Biso Wilson estimate: 53.61 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.031 / Rrim(I) all: 0.094 / Χ2: 2.086 / Net I/av σ(I): 25.6 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.349.70.57111360.9180.1920.6030.65999.9
2.34-2.389.70.50211380.930.1690.5310.72100
2.38-2.439.50.46911810.940.160.4960.757100
2.43-2.488.70.411220.9480.1440.4260.887100
2.48-2.5390.3411160.9610.1190.360.9599.9
2.53-2.5910.20.29411810.9760.0960.310.959100
2.59-2.6610.20.2611320.9780.0850.2741.088100
2.66-2.73100.24811400.980.0820.2611.311100
2.73-2.819.90.19111690.9820.0630.2011.375100
2.81-2.99.90.16811500.9860.0560.1771.641100
2.9-39.80.15511670.9910.0520.1641.88799.8
3-3.129.60.13411430.9880.0460.1422.155100
3.12-3.268.40.11911580.990.0440.1272.544100
3.26-3.449.90.10511570.9950.0350.1112.964100
3.44-3.659.90.09611660.9960.0320.1013.272100
3.65-3.939.60.08711720.9970.0290.0923.648100
3.93-4.339.30.07711860.9960.0260.0823.865100
4.33-4.958.20.07111810.9970.0260.0763.8499.9
4.95-6.249.60.07212110.9970.0240.0763.56799.9
6.24-508.30.06512900.9950.0240.0693.85499.5

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W2O

5w2o


Resolution: 2.305→39.519 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.01
RfactorNum. reflection% reflection
Rfree0.2043 2005 8.62 %
Rwork0.1712 --
obs0.1741 23255 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 154.41 Å2 / Biso mean: 63.2467 Å2 / Biso min: 32.35 Å2
Refinement stepCycle: final / Resolution: 2.305→39.519 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3024 0 46 77 3147
Biso mean--72.4 56.68 -
Num. residues----414
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3049-2.36250.29351380.22691450158896
2.3625-2.42640.26171410.222114961637100
2.4264-2.49770.29411370.21614911628100
2.4977-2.57830.23641350.206815081643100
2.5783-2.67050.22891430.198915021645100
2.6705-2.77740.21731410.196515101651100
2.7774-2.90370.19651420.204114921634100
2.9037-3.05680.30761390.210615111650100
3.0568-3.24820.23381460.215615111657100
3.2482-3.49890.25311410.194615221663100
3.4989-3.85070.2121470.167115221669100
3.8507-4.40730.16581430.143615281671100
4.4073-5.55030.15621530.144115711724100
5.5503-39.52430.18671590.147716361795100
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)
10.6479-0.5655-0.18612.4838-0.78280.64620.29550.2318-0.17120.0647-0.32090.01730.34160.31280.01890.5234-0.0555-0.03020.46530.04080.435841.0796-16.6596-14.3099
20.51610.19070.03251.8574-0.80430.47080.15380.0450.114-0.3219-0.423-0.08490.38560.2937-0.11040.57640.1126-0.03790.44640.01790.439942.9317-10.9105-29.9542
30.48690.2838-0.01743.2507-1.02411.0270.3291-0.0354-0.03590.4062-0.27470.3264-0.16360.13460.03960.5107-0.10320.07130.3099-0.05720.371131.6812-6.3596-11.7416
40.80350.20490.5371.3278-0.750.84520.3497-0.20760.04110.7056-0.25490.4626-0.18060.10640.06890.7752-0.21790.16750.4051-0.05480.494428.8725-11.5404-2.7059
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 81 )A3 - 81
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 148 )A82 - 148
3X-RAY DIFFRACTION3chain 'A' and (resid 149 through 329 )A149 - 329
4X-RAY DIFFRACTION4chain 'A' and (resid 330 through 416 )A330 - 416

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