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- PDB-5w2q: Crystal structure of Mycobacterium tuberculosis KasA in complex w... -

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Basic information

Entry
Database: PDB / ID: 5w2q
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 / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytosol
Similarity search - Function
Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / 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 ...Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / 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 / 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: 1.8 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
Water3,603200
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 area8040 Å2
ΔGint-38 kcal/mol
Surface area25720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.289, 77.289, 145.126
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-690-

HOH

21A-713-

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 (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, 208 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.: 200 / 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: 57.59 %
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 26, 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: 1.8→50 Å / Num. obs: 47310 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 30.14 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.02 / Rrim(I) all: 0.054 / Χ2: 1.158 / Net I/av σ(I): 38.5 / Net I/σ(I): 12.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.837.30.8472.30.7570.3380.9130.952100
1.83-1.867.30.7050.8320.2810.7590.953100
1.86-1.97.30.6190.8640.2470.6671.066100
1.9-1.947.20.5660.8910.2270.611.334100
1.94-1.987.30.3930.9350.1560.4231.123100
1.98-2.037.30.2980.9630.1180.3211.137100
2.03-2.087.30.270.9690.1080.2911.366100
2.08-2.137.30.1990.9830.0790.2141.218100
2.13-2.27.40.1660.9860.0660.1791.263100
2.2-2.277.30.1740.9820.070.1881.497100
2.27-2.357.30.1240.9930.0490.1331.299100
2.35-2.447.40.10.9950.0390.1071.314100
2.44-2.557.30.0850.9960.0330.0911.222100
2.55-2.697.30.0740.9950.0290.081.24100
2.69-2.867.40.0620.9980.0240.0661.237100
2.86-3.087.30.0580.9970.0230.0631.409100
3.08-3.397.30.0440.9990.0170.0471.147100
3.39-3.887.30.0340.9990.0130.0370.911100
3.88-4.887.20.0250.9990.010.0270.7699.9
4.88-506.90.0210.0080.0220.73399.8

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C6U

4c6u


Resolution: 1.8→49.199 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.93
RfactorNum. reflection% reflection
Rfree0.1862 1990 4.21 %
Rwork0.1557 --
obs0.157 47247 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.43 Å2 / Biso mean: 37.127 Å2 / Biso min: 19.94 Å2
Refinement stepCycle: final / Resolution: 1.8→49.199 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3024 0 71 200 3295
Biso mean--54.85 41.46 -
Num. residues----414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063173
X-RAY DIFFRACTIONf_angle_d0.8324314
X-RAY DIFFRACTIONf_chiral_restr0.056475
X-RAY DIFFRACTIONf_plane_restr0.005571
X-RAY DIFFRACTIONf_dihedral_angle_d15.5411883
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8001-1.84510.29291400.231931983338
1.8451-1.8950.24761370.216231693306
1.895-1.95080.29571420.228331893331
1.9508-2.01370.22461390.178731713310
2.0137-2.08570.22451450.172532293374
2.0857-2.16920.20791370.158231873324
2.1692-2.2680.19311410.165532113352
2.268-2.38750.16421440.160432023346
2.3875-2.53710.2271400.160432193359
2.5371-2.7330.24091450.167232373382
2.733-3.0080.18311410.166532263367
3.008-3.44310.17781450.156332693414
3.4431-4.33760.16891460.134333053451
4.3376-49.21770.14721480.138434453593
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)
11.89740.37360.26211.1917-0.03171.44710.142-0.0467-0.19350.1233-0.04210.26990.2741-0.1442-0.09170.3235-0.09250.01710.17970.00060.313626.4192-17.3551-13.1708
21.711-0.5184-0.27060.28750.29611.46410.0295-0.516-0.47570.3075-0.3452-0.3890.67010.27490.14440.4827-0.0238-0.09290.26630.10360.352547.4234-18.4983-3.4409
36.55913.66440.96337.2281.12413.07470.5874-0.1548-0.26420.5178-0.5903-1.17820.71981.096-0.04710.38840.0438-0.06420.62670.16750.718860.919-10.6532-8.7777
42.71681.38731.13762.11311.53812.7720.2787-0.3873-0.37050.5634-0.2583-0.64620.24350.21730.00950.3842-0.052-0.11620.30260.05960.342151.2923-13.2589-6.6978
52.2465-0.67050.39093.13510.64231.70690.18070.325-0.2144-0.3039-0.3003-0.39510.73140.2720.11720.43160.11440.03290.28650.02920.320147.6449-18.0269-26.6699
65.91682.07170.68561.87620.18091.5164-0.02780.1258-0.9351-0.34520.027-0.17890.8327-0.0011-0.0470.55330.0053-0.0280.2099-0.0370.33133.3155-22.5567-24.7688
73.0256-3.2451.93435.5412-4.20963.45780.16860.3763-0.4185-0.42180.06850.50080.9047-0.2133-0.14990.5456-0.0218-0.110.2978-0.08070.399423.2065-19.729-34.171
81.68340.14080.12661.5677-0.10541.08970.1235-0.1560.1808-0.1328-0.2404-0.02420.05020.02350.11210.27680.0161-0.01950.183-0.0040.247139.2814-7.5073-26.1698
96.1370.3211-0.22294.1191-3.50846.2810.0251-0.1634-1.05360.0436-0.3642-0.97720.07870.75590.35620.33650.03340.03140.42820.08340.590359.7361-2.7918-34.7323
100.7547-0.243-0.21141.7788-0.55560.80790.16720.04370.0561-0.1057-0.1740.06150.0750.01080.0050.29290.0064-0.00810.1905-0.02750.247634.7848-7.519-24.7354
113.0393-0.82780.15653.2488-0.30262.10790.2857-0.3780.17130.97860.0549-0.3865-0.26930.1846-0.24820.5437-0.1135-0.09450.3382-0.00760.366749.4409-2.401-1.9226
124.4637-0.3393-2.86855.2255-2.4643.22480.081-0.7889-0.36430.778-0.1397-0.50880.34940.9005-0.06920.7251-0.1156-0.21670.54570.13080.433948.5932-15.25045.0551
134.4569-2.1483-0.14181.72950.75151.73240.1235-0.9508-0.19251.0899-0.17010.1768-0.17240.2253-0.05550.7065-0.1895-0.03770.36810.03620.289839.7905-7.5026.5241
140.68970.1759-0.23661.5988-0.80250.51090.1844-0.0344-0.00050.2822-0.1830.05240.15760.02580.03250.3196-0.0451-0.00230.212-0.03580.242435.7749-11.5526-11.8997
152.67980.43440.7712.97631.98344.37450.26770.0533-0.7091-0.24730.03560.75280.6214-0.824-0.24320.4545-0.1624-0.07960.331-0.03590.528716.0768-22.0373-22.649
160.4120.22350.05951.7742-0.43951.41880.1894-0.18290.06890.5811-0.13280.3238-0.1444-0.1008-0.06390.3888-0.06830.10660.2186-0.03890.284325.8394-0.5646-5.841
172.87770.7855-0.6272.8288-3.31473.95490.1338-0.53650.48770.8620.18680.1767-0.4275-0.2877-0.32110.5336-0.0680.18040.313-0.0730.444520.7282-1.22012.9016
180.12090.11050.08720.9412-0.41740.55140.1686-0.2179-0.01270.3834-0.17840.15530.07750.0382-0.00540.4077-0.10460.02770.22660.00320.260831.6508-14.586-5.3711
195.9602-2.23831.84675.1905-0.61912.990.0505-0.34730.61651.1888-0.3820.1354-0.0777-0.26420.22930.881-0.21210.07120.41710.00040.349434.0752-5.521510.9881
200.4217-0.55350.24871.3118-0.52141.53920.1495-0.1592-0.08730.4737-0.08050.30720.0359-0.1619-0.02350.4235-0.12270.09290.2477-0.01270.314524.9549-10.9032-4.2239
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 3:39)A3 - 39
2X-RAY DIFFRACTION2(chain A and resid 40:46)A40 - 46
3X-RAY DIFFRACTION3(chain A and resid 47:55)A47 - 55
4X-RAY DIFFRACTION4(chain A and resid 56:65)A56 - 65
5X-RAY DIFFRACTION5(chain A and resid 66:86)A66 - 86
6X-RAY DIFFRACTION6(chain A and resid 87:99)A87 - 99
7X-RAY DIFFRACTION7(chain A and resid 100:106)A100 - 106
8X-RAY DIFFRACTION8(chain A and resid 107:123)A107 - 123
9X-RAY DIFFRACTION9(chain A and resid 124:137)A124 - 137
10X-RAY DIFFRACTION10(chain A and resid 138:209)A138 - 209
11X-RAY DIFFRACTION11(chain A and resid 210:220)A210 - 220
12X-RAY DIFFRACTION12(chain A and resid 221:225)A221 - 225
13X-RAY DIFFRACTION13(chain A and resid 226:233)A226 - 233
14X-RAY DIFFRACTION14(chain A and resid 234:250)A234 - 250
15X-RAY DIFFRACTION15(chain A and resid 251:262)A251 - 262
16X-RAY DIFFRACTION16(chain A and resid 263:326)A263 - 326
17X-RAY DIFFRACTION17(chain A and resid 327:333)A327 - 333
18X-RAY DIFFRACTION18(chain A and resid 334:372)A334 - 372
19X-RAY DIFFRACTION19(chain A and resid 373:381)A373 - 381
20X-RAY DIFFRACTION20(chain A and resid 382:416)A382 - 416

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