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- PDB-2wgf: Crystal structure of Mycobacterium tuberculosis C171Q KasA variant -

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Basic information

Entry
Database: PDB / ID: 2wgf
TitleCrystal structure of Mycobacterium tuberculosis C171Q KasA variant
Components3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1
KeywordsTRANSFERASE / BETA KETOACYL SYNTHASE I / CYTOPLASM / ACYLTRANSFERASE / 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 / fatty acid elongation / acyltransferase activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / peptidoglycan-based cell wall / fatty acid biosynthetic process / identical protein binding / plasma membrane / cytosol / 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
DI(HYDROXYETHYL)ETHER / 3-oxoacyl-[acyl-carrier-protein] synthase 1 / 3-oxoacyl-[acyl-carrier-protein] synthase 1
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsLuckner, S.R. / Kisker, C.
CitationJournal: Structure / Year: 2009
Title: Crystal Structures of Mycobacterium Tuberculosis Kasa Show Mode of Action within Cell Wall Biosynthesis and its Inhibition by Thiolactomycin
Authors: Luckner, S.R. / Machutta, C.A. / Tonge, P.J. / Kisker, C.
History
DepositionApr 17, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1
B: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1
C: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1
D: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1
E: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1
F: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1
G: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1
H: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)348,72924
Polymers347,0808
Non-polymers1,65016
Water63135
1
A: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1
B: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3997
Polymers86,7702
Non-polymers6295
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8520 Å2
ΔGint-55.3 kcal/mol
Surface area25810 Å2
MethodPISA
2
C: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1
D: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3107
Polymers86,7702
Non-polymers5415
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8270 Å2
ΔGint-52.6 kcal/mol
Surface area25910 Å2
MethodPISA
3
E: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1
F: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2046
Polymers86,7702
Non-polymers4344
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7820 Å2
ΔGint-42.7 kcal/mol
Surface area25950 Å2
MethodPISA
4
G: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1
H: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,8164
Polymers86,7702
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-78.6 kcal/mol
Surface area26420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.505, 151.505, 147.839
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.77834, 0.6274, -0.02363), (0.62772, 0.77689, -0.04913), (-0.01247, -0.05308, -0.99851)6.10169, -2.11198, -2.89228
2given(0.99859, -0.0232, 0.04772), (-0.02254, -0.99964, -0.0143), (0.04803, 0.0132, -0.99876)40.62075, 71.63598, -54.68475
3given(-0.79584, 0.60216, -0.06354), (-0.60544, -0.79291, 0.06881), (-0.00894, 0.09323, 0.9956)46.82493, 73.76182, -51.70377
4given(0.9246, 0.37503, -0.06689), (0.37967, -0.92155, 0.08123), (-0.03118, -0.1005, -0.99445)-50.74939, 57.00447, -50.4523
5given(-0.47879, 0.87731, 0.03286), (-0.87787, -0.478, -0.02914), (-0.00986, -0.0428, 0.99904)-45.99259, 61.19463, -47.95533
6given(-0.80515, 0.59192, 0.03686), (-0.59306, -0.80386, -0.0456), (0.00264, -0.05857, 0.99828)13.10724, 129.50539, -48.00977
7given(0.99762, -0.04289, -0.05399), (-0.03736, -0.99433, 0.09958), (-0.05796, -0.09732, -0.99356)6.65405, 127.74773, -50.62811

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Components

#1: Protein
3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1 / BETA KETOACYL SYNTHASE I / KAS 1 / BETA-KETOACYL-ACP SYNTHASE


Mass: 43384.969 Da / Num. of mol.: 8 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Production host: MYCOBACTERIUM SMEGMATIS (bacteria) / Strain (production host): MC2155
References: UniProt: P63454, UniProt: P9WQD9*PLUS, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 171 TO GLN ENGINEERED RESIDUE IN CHAIN B, CYS 171 TO GLN ...ENGINEERED RESIDUE IN CHAIN A, CYS 171 TO GLN ENGINEERED RESIDUE IN CHAIN B, CYS 171 TO GLN ENGINEERED RESIDUE IN CHAIN C, CYS 171 TO GLN ENGINEERED RESIDUE IN CHAIN D, CYS 171 TO GLN ENGINEERED RESIDUE IN CHAIN E, CYS 171 TO GLN ENGINEERED RESIDUE IN CHAIN F, CYS 171 TO GLN ENGINEERED RESIDUE IN CHAIN G, CYS 171 TO GLN ENGINEERED RESIDUE IN CHAIN H, CYS 171 TO GLN
Sequence detailsCYS 171 IS MUTATED TO GLN 171

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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: 2.85 Å3/Da / Density % sol: 56.83 % / Description: NONE
Crystal growDetails: PEG3350, POTASSIUM FORMATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.452
ReflectionResolution: 2.15→33.71 Å / Num. obs: 335101 / % possible obs: 97.9 % / Observed criterion σ(I): 1 / Redundancy: 1.7 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.64
Reflection shellResolution: 2.15→2.17 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.6 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
TRUNCATEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WGD

2wgd


Resolution: 2.15→33.71 Å / σ(F): 0.97 / Phase error: 22.73 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.211 16509 5.9 %
Rwork0.166 --
obs0.168 280329 67.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.52 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 55.04 Å2
Baniso -1Baniso -2Baniso -3
1--24.0188 Å20 Å20 Å2
2---24.0188 Å20 Å2
3----37.3431 Å2
Refinement stepCycle: LAST / Resolution: 2.15→33.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24256 0 106 35 24397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00524847
X-RAY DIFFRACTIONf_angle_d0.91733723
X-RAY DIFFRACTIONf_dihedral_angle_d16.918937
X-RAY DIFFRACTIONf_chiral_restr0.0613771
X-RAY DIFFRACTIONf_plane_restr0.0044502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.18710.27555450.243810966X-RAY DIFFRACTION98
2.1871-2.22680.24827180.237712505X-RAY DIFFRACTION98
2.2268-2.26970.26746000.234712493X-RAY DIFFRACTION98
2.2697-2.3160.25516360.231512716X-RAY DIFFRACTION98
2.316-2.36630.25536530.217112745X-RAY DIFFRACTION98
2.3663-2.42140.24635150.21912958X-RAY DIFFRACTION98
2.4214-2.48190.306590.211913736X-RAY DIFFRACTION98
2.4819-2.5490.263112240.204712567X-RAY DIFFRACTION98
2.549-2.6240.26610260.198512733X-RAY DIFFRACTION98
2.624-2.70860.23851930.190513789X-RAY DIFFRACTION98
2.7086-2.80540.250911000.18812902X-RAY DIFFRACTION98
2.8054-2.91760.24199610.180513235X-RAY DIFFRACTION98
2.9176-3.05030.22097030.169813569X-RAY DIFFRACTION98
3.0503-3.2110.21571930.164814342X-RAY DIFFRACTION98
3.211-3.4120.21649190.153413643X-RAY DIFFRACTION98
3.412-3.67520.207911830.144113479X-RAY DIFFRACTION98
3.6752-4.04450.18565600.130414315X-RAY DIFFRACTION98
4.0445-4.62850.15089300.112814173X-RAY DIFFRACTION98
4.6285-5.82650.17176400.13614635X-RAY DIFFRACTION98
5.8265-33.71280.17959570.157814563X-RAY DIFFRACTION98

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