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- PDB-5w2p: Crystal structure of Mycobacterium tuberculosis KasA in complex w... -

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Basic information

Entry
Database: PDB / ID: 5w2p
TitleCrystal structure of Mycobacterium tuberculosis KasA in complex with 6U5
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 / acyltransferase activity, transferring groups other than amino-acyl groups / fatty acid biosynthetic process / cytoplasm
Similarity search - Function
Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / 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 ...Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
~{N}-(1-methylindazol-6-yl)butane-1-sulfonamide / ISOPROPYL ALCOHOL / 3,3',3''-phosphanetriyltripropanoic acid / 3-oxoacyl-[acyl-carrier-protein] synthase 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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: MBio / Year: 2018
Title: Synergistic Lethality of a Binary Inhibitor of Mycobacterium tuberculosis KasA.
Authors: Kumar, P. / Capodagli, G.C. / Awasthi, D. / Shrestha, R. / Maharaja, K. / Sukheja, P. / Li, S.G. / Inoyama, D. / Zimmerman, M. / Ho Liang, H.P. / Sarathy, J. / Mina, M. / Rasic, G. / Russo, ...Authors: Kumar, P. / Capodagli, G.C. / Awasthi, D. / Shrestha, R. / Maharaja, K. / Sukheja, P. / Li, S.G. / Inoyama, D. / Zimmerman, M. / Ho Liang, H.P. / Sarathy, J. / Mina, M. / Rasic, G. / Russo, R. / Perryman, A.L. / Richmann, T. / Gupta, A. / Singleton, E. / Verma, S. / Husain, S. / Soteropoulos, P. / Wang, Z. / Morris, R. / Porter, G. / Agnihotri, G. / Salgame, P. / Ekins, S. / Rhee, K.Y. / Connell, N. / Dartois, V. / Neiditch, M.B. / Freundlich, J.S. / Alland, D.
History
DepositionJun 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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)46,8699
Polymers45,7891
Non-polymers1,0808
Water2,936163
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)93,73818
Polymers91,5772
Non-polymers2,16016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area8140 Å2
ΔGint-37 kcal/mol
Surface area25420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.298, 77.298, 145.208
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-666-

HOH

21A-722-

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: 45788.625 Da / Num. of mol.: 1 / Mutation: M24V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 35801 / TMC 107 / Erdman) (bacteria)
Strain: ATCC 35801 / TMC 107 / Erdman / Gene: kasA, ERDMAN_2470
Production host: Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: H8ESN0, beta-ketoacyl-[acyl-carrier-protein] synthase I

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Non-polymers , 6 types, 171 molecules

#2: Chemical ChemComp-6U5 / ~{N}-(1-methylindazol-6-yl)butane-1-sulfonamide


Mass: 267.347 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H17N3O2S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Chemical ChemComp-TCE / 3,3',3''-phosphanetriyltripropanoic acid / 3-[bis(2-carboxyethyl)phosphanyl]propanoic acid


Mass: 250.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15O6P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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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: 2.9 Å3/Da / Density % sol: 57.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 200mM NaCl, 8% Isopropanol, 1mM Tris(2-carboxyethyl)phosphine hydrochloride (TCEP HCl)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.1808 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 25, 2016
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1808 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 34892 / % possible obs: 99 % / Redundancy: 6.3 % / Biso Wilson estimate: 36.23 Å2 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.019 / Rrim(I) all: 0.051 / Χ2: 1.191 / Net I/σ(I): 15.1 / Num. measured all: 219551
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.036.10.62717320.8310.2660.6861.12399.3
2.03-2.076.20.4830.8790.2040.5281.1298.9
2.07-2.116.20.4340.8840.1830.4741.14797.7
2.11-2.156.20.360.9310.1510.3931.17397.8
2.15-2.26.20.2920.9470.1220.3191.18299.8
2.2-2.256.30.2710.9520.1140.2961.22898.3
2.25-2.316.30.2160.9680.090.2351.25698.8
2.31-2.376.30.1740.9810.0720.1891.25399
2.37-2.446.20.1530.9840.0640.1671.28999.7
2.44-2.526.30.1230.990.0510.1341.31499.5
2.52-2.616.30.0990.9940.0410.1081.23699.5
2.61-2.716.30.0890.9940.0370.0971.21799.6
2.71-2.846.30.0730.9950.030.081.24799.3
2.84-2.996.30.0650.9950.0270.071.32599.4
2.99-3.176.40.0530.9960.0220.0581.28999.4
3.17-3.426.40.0410.9970.0170.0441.31498.9
3.42-3.766.50.0340.9980.0140.0371.299.3
3.76-4.316.40.030.9990.0130.0321.06699.5
4.31-5.436.40.0270.9990.0110.0290.95898.3
5.43-506.20.0260.9990.0110.0290.998.7

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C6U

4c6u


Resolution: 2→39.224 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.91
RfactorNum. reflection% reflection
Rfree0.1856 1989 5.71 %
Rwork0.1573 --
obs0.1589 34833 98.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.02 Å2 / Biso mean: 41.7764 Å2 / Biso min: 21.11 Å2
Refinement stepCycle: final / Resolution: 2→39.224 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3024 0 71 163 3258
Biso mean--57 42.7 -
Num. residues----414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073164
X-RAY DIFFRACTIONf_angle_d0.8214300
X-RAY DIFFRACTIONf_chiral_restr0.055474
X-RAY DIFFRACTIONf_plane_restr0.005569
X-RAY DIFFRACTIONf_dihedral_angle_d7.9682539
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 (%)
1.983-2.03260.23071200.20111988210885
2.0326-2.08760.21491440.18672317246198
2.0876-2.1490.20661400.1792318245898
2.149-2.21840.21941430.17832315245899
2.2184-2.29760.22921420.17642327246999
2.2976-2.38960.23561440.17722356250099
2.3896-2.49840.23251450.17842381252699
2.4984-2.630.2091430.179923452488100
2.63-2.79480.20931470.17982380252799
2.7948-3.01050.20681420.17472356249899
3.0105-3.31330.21481450.17022391253699
3.3133-3.79240.18081430.1522402254599
3.7924-4.77670.14011410.12642423256499
4.7767-39.23120.15471500.14222545269599
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)
10.7878-0.1770.18350.2394-0.27991.04470.36460.05610.133-0.0672-0.16190.21060.3237-0.11740.08920.2894-0.0804-0.00390.20920.00170.482522.486-13.6304-16.5889
20.1222-0.04220.1110.0288-0.0390.07390.19230.224-0.510.4371-0.01570.04710.36920.32010.0040.4847-0.0771-0.01220.23440.06150.340336.2138-23.337-5.5671
30.0046-0.0211-0.02740.05170.04760.04950.08850.1980.0320.0945-0.1273-0.22140.4290.391-0.00360.39270.0032-0.10920.53450.20340.619858.0962-13.6875-7.8903
40.2606-0.0774-0.14120.14240.23330.33550.223-0.1905-0.33020.5189-0.2911-0.58170.25110.3351-0.17520.4429-0.0724-0.15540.40760.10660.390453.9105-11.3642-6.9111
50.19390.20960.18620.20770.24840.23110.12580.1712-0.022-0.2148-0.3732-0.14960.58190.169-0.01430.49450.16080.03840.33180.05160.324148.3947-18.6862-26.9764
60.3410.1451-0.56580.2122-0.45281.23990.2712-0.1819-0.0202-0.455-0.49020.09770.86010.679-0.13260.54650.0544-0.0681-0.0104-0.08360.294834.1732-21.3324-25.8942
70.1479-0.0296-0.22490.4891-0.30760.27990.1518-0.05630.0418-0.2796-0.22350.08550.14570.0152-0.010.33790.0302-0.07850.2213-0.03650.295834.8352-9.5084-28.3029
80.0322-0.0187-0.0320.0685-0.03660.02240.3422-0.0866-0.66240.11580.0782-0.5604-0.01040.41540.00780.45420.0291-0.02090.58280.12450.635259.8326-2.8162-33.9874
90.29960.12370.01911.759-0.5740.4110.1393-0.01670.05-0.1486-0.16490.14710.1702-0.0080.01390.31410.0281-0.03140.183-0.03230.25233.2786-7.7946-26.219
100.31740.0154-0.24040.064-0.02280.09980.1991-0.08290.23380.437-0.0409-0.4316-0.01660.01290.00820.5178-0.1671-0.08940.36630.04360.411550.7083-3.0253-5.2839
110.213-0.11950.05170.3581-0.01780.0132-0.0276-0.1939-0.03620.1225-0.2794-0.16390.00640.2554-0.22260.9834-0.2691-0.35390.59920.28250.187748.7649-15.04025.1328
120.6213-0.0073-0.03781.277-0.86910.4580.2488-0.0652-0.17030.4983-0.20510.12510.08420.09830.02550.4413-0.10730.01080.2743-0.00450.270136.0735-10.533-6.3684
130.172-0.15890.08980.1973-0.120.05830.0999-0.1897-0.4571-0.26070.10921.00680.291-0.30770.26680.459-0.1792-0.1590.2815-0.06790.695916.5702-21.6113-21.273
140.0666-0.08760.18340.2785-0.41880.32480.1176-0.09620.00720.5906-0.06620.3304-0.20630.07480.00410.4863-0.09080.11650.2561-0.06030.288829.37915.0341-8.3992
150.00620.01160.02180.00910.00370.00520.1131-0.22280.30140.4723-0.13450.3535-0.1799-0.17800.4298-0.01870.2050.2939-0.01570.526618.67960.6064-9.2659
160.2684-0.008-0.0830.2637-0.20120.40690.2559-0.17410.10610.8995-0.1730.3962-0.0351-0.04220.06310.5798-0.13510.16110.2703-0.01440.370626.3403-4.1487-2.1876
170.00520.0006-0.01520.0167-0.00770.00750.1108-0.32560.22710.23810.11410.3099-0.1875-0.207500.6288-0.08340.25070.3162-0.08670.479721.3662-1.25642.6378
180.1382-0.08840.21040.1745-0.19850.14450.1991-0.19950.02920.3368-0.13480.19890.00370.1293-0.0050.4368-0.11740.03810.23640.00860.284331.1712-14.553-6.2576
190.16150.0658-0.01670.45190.2920.22410.2592-0.4860.08570.7956-0.1733-0.00890.0235-0.13590.04150.9903-0.21830.09780.3740.01820.312734.9093-7.56429.4362
200.2332-0.26650.18460.45920.02940.53820.1562-0.1107-0.01160.4636-0.09250.3992-0.0469-0.1531-0.08910.459-0.16160.14120.2188-0.00070.344525.0345-10.8745-4.2233
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 3:27)A3 - 27
2X-RAY DIFFRACTION2(chain A and resid 28:43)A28 - 43
3X-RAY DIFFRACTION3(chain A and resid 44:53)A44 - 53
4X-RAY DIFFRACTION4(chain A and resid 54:65)A54 - 65
5X-RAY DIFFRACTION5(chain A and resid 66:83)A66 - 83
6X-RAY DIFFRACTION6(chain A and resid 84:102)A84 - 102
7X-RAY DIFFRACTION7(chain A and resid 103:122)A103 - 122
8X-RAY DIFFRACTION8(chain A and resid 123:136)A123 - 136
9X-RAY DIFFRACTION9(chain A and resid 137:202)A137 - 202
10X-RAY DIFFRACTION10(chain A and resid 203:220)A203 - 220
11X-RAY DIFFRACTION11(chain A and resid 221:225)A221 - 225
12X-RAY DIFFRACTION12(chain A and resid 226:251)A226 - 251
13X-RAY DIFFRACTION13(chain A and resid 252:264)A252 - 264
14X-RAY DIFFRACTION14(chain A and resid 265:288)A265 - 288
15X-RAY DIFFRACTION15(chain A and resid 289:296)A289 - 296
16X-RAY DIFFRACTION16(chain A and resid 297:325)A297 - 325
17X-RAY DIFFRACTION17(chain A and resid 326:333)A326 - 333
18X-RAY DIFFRACTION18(chain A and resid 334:369)A334 - 369
19X-RAY DIFFRACTION19(chain A and resid 370:381)A370 - 381
20X-RAY DIFFRACTION20(chain A and resid 382:416)A382 - 416

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