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- PDB-5w2s: Crystal Structure of Mycobacterium Tuberculosis KasA in complex w... -

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Basic information

Entry
Database: PDB / ID: 5w2s
TitleCrystal Structure of Mycobacterium Tuberculosis KasA in complex with KMG
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
ISOPROPYL ALCOHOL / N-(3-methyl-2H-indazol-5-yl)butane-1-sulfonamide / 3-oxoacyl-[acyl-carrier-protein] synthase 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.399 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)46,3236
Polymers45,7891
Non-polymers5355
Water1,42379
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)92,64612
Polymers91,5772
Non-polymers1,06910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area7280 Å2
ΔGint-51 kcal/mol
Surface area26020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.038, 77.038, 145.807
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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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 , 5 types, 84 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.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-KMG / N-(3-methyl-2H-indazol-5-yl)butane-1-sulfonamide


Mass: 267.347 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H17N3O2S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 57.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 200mM NaCl, 4% 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: BL9-2 / Wavelength: 0.88557 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2016
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88557 Å / Relative weight: 1
ReflectionResolution: 2.399→50 Å / Num. obs: 20269 / % possible obs: 100 % / Redundancy: 9.7 % / Biso Wilson estimate: 48.98 Å2 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.024 / Rrim(I) all: 0.074 / Χ2: 0.734 / Net I/σ(I): 6.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.449.70.5883.70.9460.1980.6210.444100
2.44-2.499.20.5410.9410.1870.5730.448100
2.49-2.538.30.4060.950.1490.4340.45199.8
2.53-2.599.10.3730.9670.130.3960.449100
2.59-2.6410.50.3680.9790.1180.3870.501100
2.64-2.710.10.510.8780.1740.541.761100
2.7-2.7710.40.2310.9880.0750.2430.47299.9
2.77-2.8510.40.1820.9920.0590.1920.47599.9
2.85-2.9310.30.1520.9940.050.160.476100
2.93-3.0210.20.1250.9940.0410.1320.488100
3.02-3.1310.10.1040.9970.0340.110.495100
3.13-3.26100.0880.9970.0290.0930.532100
3.26-3.419.70.0710.9980.0240.0740.585100
3.41-3.588.90.1050.9950.0380.1121.441100
3.58-3.818.10.0870.990.0340.0931.50799.8
3.81-4.110.10.0740.9930.0250.0781.413100
4.1-4.5210.20.0440.9990.0140.0460.77699.9
4.52-5.17100.0440.9990.0150.0470.811100
5.17-6.519.30.0390.9990.0130.0420.64699.9
6.51-508.90.0310.010.0320.64899.9

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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: 5W2O

5w2o


Resolution: 2.399→49.218 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.36
RfactorNum. reflection% reflection
Rfree0.2137 2002 9.9 %
Rwork0.1841 --
obs0.1871 20221 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 148.09 Å2 / Biso mean: 58.7284 Å2 / Biso min: 32.31 Å2
Refinement stepCycle: final / Resolution: 2.399→49.218 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3024 0 35 79 3138
Biso mean--57.73 48.88 -
Num. residues----414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033144
X-RAY DIFFRACTIONf_angle_d0.5524279
X-RAY DIFFRACTIONf_chiral_restr0.044478
X-RAY DIFFRACTIONf_plane_restr0.004569
X-RAY DIFFRACTIONf_dihedral_angle_d9.772535
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 (%)
2.3993-2.45930.26081380.22751256139499
2.4593-2.52570.2881440.234712751419100
2.5257-2.60010.23341400.234612851425100
2.6001-2.6840.26651370.269712771414100
2.684-2.77990.24381420.234912941436100
2.7799-2.89120.24451400.215512731413100
2.8912-3.02280.2511430.21612951438100
3.0228-3.18210.24751460.212612951441100
3.1821-3.38140.24661420.204212951437100
3.3814-3.64240.22671450.206512961441100
3.6424-4.00880.24771390.176513081447100
4.0088-4.58860.20261420.151513201462100
4.5886-5.77970.16111440.153913321476100
5.7797-49.22840.16631600.150414181578100
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)
12.20681.19511.13050.89760.71461.1286-0.0722-0.36030.0759-0.2204-0.0139-0.1653-0.59230.3112-0.03490.3716-0.0025-0.01040.46-0.04950.397932.5588-23.1615-38.5234
21.65770.69960.70710.56480.56140.857-0.3613-0.0972-0.0568-0.23210.2320.0664-0.26260.1757-0.03240.4261-0.10620.02880.3846-0.02680.390527.9009-28.83-52.3657
32.65781.10320.73241.54760.64281.54910.1689-0.832-0.24490.1492-0.0831-0.18780.0779-0.140.09440.3255-0.0452-0.03990.63350.10.414228.1164-36.0614-31.9409
41.03480.40090.28820.65160.38260.65520.1703-0.7033-0.35170.1365-0.0326-0.23950.0762-0.13320.02450.3379-0.0632-0.08210.81520.13050.489234.7126-36.5958-27.1426
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 186 )A82 - 186
3X-RAY DIFFRACTION3chain 'A' and (resid 187 through 346 )A187 - 346
4X-RAY DIFFRACTION4chain 'A' and (resid 347 through 416 )A347 - 416

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