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- PDB-6p9k: Crystal structure of Mycobacterium tuberculosis KasA in complex w... -

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Basic information

Entry
Database: PDB / ID: 6p9k
TitleCrystal structure of Mycobacterium tuberculosis KasA in complex with O6G
Components3-oxoacyl-ACP synthase
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 / beta-ketoacyl-[acyl-carrier-protein] synthase II / beta-ketoacyl-[acyl-carrier-protein] synthase I / fatty acid elongation / 3-oxoacyl-[acyl-carrier-protein] synthase activity / peptidoglycan-based cell wall / fatty acid biosynthetic process / identical protein binding / plasma membrane ...meromycolic acid 3-oxoacyl-(acyl carrier protein) synthase I / fatty acid elongation, saturated fatty acid / beta-ketoacyl-[acyl-carrier-protein] synthase II / beta-ketoacyl-[acyl-carrier-protein] synthase I / fatty acid elongation / 3-oxoacyl-[acyl-carrier-protein] synthase activity / peptidoglycan-based cell wall / fatty acid biosynthetic process / identical protein binding / plasma membrane / cytoplasm / 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-O6G / 3-oxoacyl-ACP synthase / 3-oxoacyl-[acyl-carrier-protein] synthase 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.703 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-ACP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8499
Polymers43,1421
Non-polymers7078
Water5,170287
1
A: 3-oxoacyl-ACP synthase
hetero molecules

A: 3-oxoacyl-ACP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,69718
Polymers86,2832
Non-polymers1,41416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area8240 Å2
ΔGint-36 kcal/mol
Surface area26260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.505, 77.505, 145.167
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-717-

HOH

21A-747-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 3-oxoacyl-ACP synthase


Mass: 43141.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: kasA_2, kasA, kasA_1, ERS007663_00367, ERS007672_01613, ERS007679_01974, ERS007681_02066, ERS007688_01478, ERS007703_02203, ERS007722_03184, ERS007741_02349, ERS023446_01403, ERS024276_01522, ...Gene: kasA_2, kasA, kasA_1, ERS007663_00367, ERS007672_01613, ERS007679_01974, ERS007681_02066, ERS007688_01478, ERS007703_02203, ERS007722_03184, ERS007741_02349, ERS023446_01403, ERS024276_01522, ERS027644_00736, ERS027646_00897, ERS027651_00106, ERS027652_01351, ERS027656_00221, ERS027659_01260, ERS027666_02494, ERS031537_00603, ERS124361_03146, SAMEA2683035_01249
Production host: Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0A045JQD6, UniProt: P9WQD9*PLUS, beta-ketoacyl-[acyl-carrier-protein] synthase I

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Non-polymers , 5 types, 295 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O
#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-O6G / N-(2-cyano-3-methyl-1H-indol-5-yl)butane-1-sulfonamide


Mass: 291.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H17N3O2S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.92 Å3/Da / Density % sol: 57.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 200mM NaCl, 6% Isopropanol, 1mM Tris(2-carboxyethyl)phosphine hydrochloride (TCEP HCl)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.88557 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2017
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88557 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 56051 / % possible obs: 100 % / Redundancy: 9.9 % / Biso Wilson estimate: 28 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.022 / Rrim(I) all: 0.068 / Χ2: 0.934 / Net I/av σ(I): 20.2 / Net I/σ(I): 7.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.7310.20.54627640.9080.1790.5750.488100
1.73-1.7610.20.43827550.9440.1430.4610.453100
1.76-1.79100.37127730.9590.1230.3910.47100
1.79-1.83100.327540.9710.0990.3160.493100
1.83-1.879.80.26627630.9760.0890.2810.506100
1.87-1.919.70.26327950.9780.0890.2780.67499.9
1.91-1.968.80.20727460.9840.0730.220.622100
1.96-2.029.70.15827620.990.0530.1670.651100
2.02-2.0710.30.15327960.9920.050.1610.817100
2.07-2.1410.30.12527800.9930.0410.1310.776100
2.14-2.2210.10.11228090.9940.0370.1180.848100
2.22-2.3110.10.10727550.9950.0350.1131.028100
2.31-2.41100.09228110.9950.030.0971.018100
2.41-2.5490.08327670.9960.0290.0891.11499.9
2.54-2.710.20.0828140.9960.0260.0841.227100
2.7-2.9110.40.07128210.9970.0230.0751.281100
2.91-3.210.20.06528300.9980.0210.0691.398100
3.2-3.669.30.05828390.9980.020.0611.604100
3.66-4.619.90.05328820.9980.0170.0561.765100
4.61-509.30.04630350.9990.0160.0491.37499.8

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Processing

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

5w2o


Resolution: 1.703→39.252 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 14.83
RfactorNum. reflection% reflection
Rfree0.1693 1993 3.56 %
Rwork0.1443 --
obs0.1451 55990 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.99 Å2 / Biso mean: 35.5983 Å2 / Biso min: 17.67 Å2
Refinement stepCycle: final / Resolution: 1.703→39.252 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3024 0 47 287 3358
Biso mean--45.34 43.77 -
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 (%)
1.7027-1.74530.19921380.16413783392199
1.7453-1.79250.16581380.153938273965100
1.7925-1.84520.17631430.14638103953100
1.8452-1.90480.17931420.15137803922100
1.9048-1.97290.18061420.150238333975100
1.9729-2.05190.15511420.140538083950100
2.0519-2.14520.18011420.143138413983100
2.1452-2.25830.16151440.140838293973100
2.2583-2.39980.21291380.153338333971100
2.3998-2.58510.18461420.150538694011100
2.5851-2.84510.17491390.156838503989100
2.8451-3.25670.18821450.153139114056100
3.2567-4.10240.1651460.134939354081100
4.1024-39.26260.1451520.136940884240100
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)
12.28080.0563-0.57552.1560.43161.36510.1803-0.05170.25270.1269-0.1549-0.0582-0.2478-0.0443-0.04190.3356-0.0448-0.02470.1590.01570.2285-36.200716.47-11.0488
21.92850.6288-0.59252.8042-0.30724.40820.16080.23090.1501-0.1782-0.21770.3996-0.4837-0.39960.04530.35880.077-0.00370.2801-0.03730.3135-50.233716.9087-20.1026
32.41-0.082-0.90740.87060.2531.38530.26080.14910.2174-0.2519-0.1997-0.2344-0.4217-0.0014-0.06380.39170.02390.05490.17570.05540.2512-33.445116.3594-26.84
43.30831.02521.69081.3971.42282.9615-0.0031-0.11970.17390.003-0.23070.5914-0.0427-0.48920.24660.37360.07350.02170.3115-0.0710.4502-54.6684.4954-33.1647
50.9315-0.18810.04261.76360.36191.06960.1746-0.09590.04580.1789-0.1417-0.1948-0.03420.0245-0.03060.2859-0.0601-0.0310.14940.02990.2237-32.78816.7405-13.8464
60.9805-0.1014-0.01171.71240.66541.21440.1712-0.2397-0.00950.5028-0.1011-0.31780.04990.0728-0.06080.4298-0.126-0.09590.22180.02630.2813-28.16639.4993-2.1916
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 54 )A3 - 54
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 81 )A55 - 81
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 118 )A82 - 118
4X-RAY DIFFRACTION4chain 'A' and (resid 119 through 146 )A119 - 146
5X-RAY DIFFRACTION5chain 'A' and (resid 147 through 298 )A147 - 298
6X-RAY DIFFRACTION6chain 'A' and (resid 299 through 416 )A299 - 416

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