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- PDB-5w2o: Crystal structure of Mycobacterium tuberculosis KasA -

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Basic information

Entry
Database: PDB / ID: 5w2o
TitleCrystal structure of Mycobacterium tuberculosis KasA
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 / 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
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)46,64611
Polymers45,7891
Non-polymers85710
Water4,900272
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)93,29222
Polymers91,5772
Non-polymers1,71520
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area9860 Å2
ΔGint-61 kcal/mol
Surface area25760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.389, 77.389, 147.008
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-737-

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, 282 molecules

#2: Chemical ChemComp-NA / SODIUM ION


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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


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


Mass: 250.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15O6P
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.95 Å3/Da / Density % sol: 58.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 200mM NaCl, 14% Isopropanol, 2mM 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: 1.8→50 Å / Num. obs: 48010 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 22.03 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.03 / Rrim(I) all: 0.077 / Χ2: 1.198 / Net I/av σ(I): 27.5 / Net I/σ(I): 10.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allRsym valueΧ2% possible all
1.8-1.836.63.523390.8750.2780.7290.6731.048100
1.83-1.866.60.9050.2320.6071.099100
1.86-1.96.70.9210.2150.5631.18100
1.9-1.946.60.9170.2050.5361.388100
1.94-1.986.70.950.1470.3841.235100
1.98-2.036.70.9650.1170.3071.221100
2.03-2.086.70.9730.1060.2741.278100
2.08-2.136.70.9790.0880.231.277100
2.13-2.26.70.9840.0750.1951.301100
2.2-2.276.70.9810.0760.1981.296100
2.27-2.356.70.9910.0570.151.363100
2.35-2.446.70.9920.0490.1291.316100
2.44-2.556.70.9950.0410.1081.299100
2.55-2.696.70.9950.0390.1011.225100
2.69-2.866.80.9960.0320.0841.155100
2.86-3.086.70.9970.0270.0711.311100
3.08-3.396.80.9980.0210.0561.171100
3.39-3.886.70.9990.0170.0450.96899.8
3.88-4.886.70.9990.0130.0331.04899.7
4.88-506.40.9990.0110.0280.78798

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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→39.557 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.49
RfactorNum. reflection% reflection
Rfree0.1789 2000 4.17 %
Rwork0.1536 --
obs0.1547 47977 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.11 Å2 / Biso mean: 28.1589 Å2 / Biso min: 11.2 Å2
Refinement stepCycle: final / Resolution: 1.8→39.557 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3024 0 54 272 3350
Biso mean--52.43 36.01 -
Num. residues----414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083171
X-RAY DIFFRACTIONf_angle_d0.8684309
X-RAY DIFFRACTIONf_chiral_restr0.055481
X-RAY DIFFRACTIONf_plane_restr0.005574
X-RAY DIFFRACTIONf_dihedral_angle_d13.4041899
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 (%)
1.7998-1.84480.23041410.202732533394100
1.8448-1.89460.19711390.192532183357100
1.8946-1.95040.26331420.197832433385100
1.9504-2.01340.18131410.161932343375100
2.0134-2.08530.16141420.15632433385100
2.0853-2.16880.18061410.151232573398100
2.1688-2.26750.19861440.163732643408100
2.2675-2.3870.19291420.156832443386100
2.387-2.53660.19741420.159432723414100
2.5366-2.73240.17561430.154833003443100
2.7324-3.00720.1641460.152632953441100
3.0072-3.44220.17941410.147633233464100
3.4422-4.33590.16561460.13533533499100
4.3359-39.56660.16081500.14883478362899
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)
10.17330.0073-0.29580.61430.02220.46250.08630.0378-0.0691-0.0085-0.0544-0.08850.19230.1127-0.00010.1982-0.0126-0.01490.13340.00720.156641.0338-16.5536-14.287
20.2235-0.1230.04550.3375-0.18010.31610.01340.01610.1161-0.0733-0.1-0.06940.16340.0305-0.01390.21770.0311-0.01360.13420.01250.194342.0607-11.2113-30.1547
30.23050.023-0.05090.6092-0.10350.45160.085-0.0279-0.01520.0976-0.03470.055-0.055-0.00660.03820.176-0.04860.01110.0976-0.00790.125631.5043-5.9212-10.8611
40.2168-0.04630.13310.2388-0.22740.20320.0919-0.04140.04070.1426-0.03350.06650.0096-0.02080.01170.2263-0.07510.01780.11970.00230.145928.6107-11.4274-2.908
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 158 )A82 - 158
3X-RAY DIFFRACTION3chain 'A' and (resid 159 through 328 )A159 - 328
4X-RAY DIFFRACTION4chain 'A' and (resid 329 through 416 )A329 - 416

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