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- PDB-2wgg: Crystal Structure of Mycobacterium tuberculosis C171Q KasA varian... -

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Basic information

Entry
Database: PDB / ID: 2wgg
TitleCrystal Structure of Mycobacterium tuberculosis C171Q KasA variant with bound TLM
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 / Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / 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. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / 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 / THIOLACTOMYCIN / 3-oxoacyl-[acyl-carrier-protein] synthase 1 / 3-oxoacyl-[acyl-carrier-protein] synthase 1
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 / Structure summary / 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)353,00539
Polymers347,0808
Non-polymers5,92531
Water16,754930
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)88,49012
Polymers86,7702
Non-polymers1,72010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7980 Å2
ΔGint-61.6 kcal/mol
Surface area31290 Å2
MethodPQS
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)88,1729
Polymers86,7702
Non-polymers1,4027
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7820 Å2
ΔGint-67.9 kcal/mol
Surface area31290 Å2
MethodPQS
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)88,1729
Polymers86,7702
Non-polymers1,4027
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7710 Å2
ΔGint-70.7 kcal/mol
Surface area31510 Å2
MethodPQS
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)88,1729
Polymers86,7702
Non-polymers1,4027
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8180 Å2
ΔGint-63.2 kcal/mol
Surface area31520 Å2
MethodPQS
Unit cell
Length a, b, c (Å)151.276, 151.276, 147.960
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(0.90231, 0.41759, 0.10703), (0.41708, -0.90843, 0.02819), (0.109, 0.0192, -0.99386)-27.04949, 124.57651, -6.17637
2given(-0.48193, -0.87613, 0.0116), (-0.87554, 0.481, -0.04552), (0.0343, -0.0321, -0.9989)82.44128, 2.61506, -50.92743
3given(-0.79658, 0.59913, -0.08065), (-0.59804, -0.80048, -0.03974), (-0.08837, 0.01657, 0.99595)-13.99573, 86.28628, -49.15926
4given(0.99999, 0.0013, -0.00377), (0.0015, -0.99853, 0.05424), (-0.0037, -0.05424, -0.99852)34.1417, 61.39457, 0.29388
5given(0.90419, 0.41014, 0.11927), (-0.4041, 0.91186, -0.07223), (-0.13839, 0.01711, 0.99023)7.69809, -63.57377, 0.61246
6given(0.91475, 0.40231, -0.03707), (0.40399, -0.91201, 0.07099), (-0.00525, -0.07992, -0.99679)39.11579, 123.26279, 1.92276
7given(0.9891, 0.0095, 0.14696), (-0.00234, 0.9988, -0.04884), (-0.14725, 0.04796, 0.98794)65.16272, -1.72498, -1.44624

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

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


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

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Non-polymers , 5 types, 961 molecules

#2: Chemical
ChemComp-TLM / THIOLACTOMYCIN / 4-HYDROXY-3,5-DIMETHYL-5-(2-METHYL-BUTA-1,3-DIENYL)-5H-THIOPHEN-2-ONE


Mass: 210.293 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C11H14O2S
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 930 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.84 Å3/Da / Density % sol: 56.74 % / Description: NONE
Crystal growDetails: PEG3350, POTASSIUM FORMATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.287
ReflectionResolution: 2→46.18 Å / Num. obs: 996668 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 3.89 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.35
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.85 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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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→46.16 Å / σ(F): 1.08 / Phase error: 26.89 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.179 26056 5.1 %
Rwork0.137 --
obs0.139 511630 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.68 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 29.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.5041 Å20 Å20 Å2
2--0.5041 Å20 Å2
3----7.8768 Å2
Refinement stepCycle: LAST / Resolution: 2→46.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24256 0 393 930 25579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01125223
X-RAY DIFFRACTIONf_angle_d1.53234198
X-RAY DIFFRACTIONf_dihedral_angle_d19.7669228
X-RAY DIFFRACTIONf_chiral_restr0.1073794
X-RAY DIFFRACTIONf_plane_restr0.014539
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.03450.244712900.21124275X-RAY DIFFRACTION98
2.0345-2.07150.23512400.193824506X-RAY DIFFRACTION98
2.0715-2.11140.230413050.188824165X-RAY DIFFRACTION98
2.1114-2.15450.212811800.185424350X-RAY DIFFRACTION98
2.1545-2.20130.210114600.179224239X-RAY DIFFRACTION98
2.2013-2.25250.210313200.17424100X-RAY DIFFRACTION98
2.2525-2.30880.205112980.170824272X-RAY DIFFRACTION98
2.3088-2.37130.188412780.161924409X-RAY DIFFRACTION98
2.3713-2.4410.19756060.157125010X-RAY DIFFRACTION98
2.441-2.51980.20318580.156523716X-RAY DIFFRACTION98
2.5198-2.6099000.149425488X-RAY DIFFRACTION98
2.6099-2.71440.207118140.147123796X-RAY DIFFRACTION98
2.7144-2.83790.197816000.145423955X-RAY DIFFRACTION98
2.8379-2.98750.184513920.139724194X-RAY DIFFRACTION98
2.9875-3.17460.189812640.134424282X-RAY DIFFRACTION98
3.1746-3.41970.182718240.122923814X-RAY DIFFRACTION98
3.4197-3.76360.167411500.111424460X-RAY DIFFRACTION98
3.7636-4.30790.134214960.097524145X-RAY DIFFRACTION98
4.3079-5.42620.137514240.095824128X-RAY DIFFRACTION98
5.4262-46.16980.150812550.127624272X-RAY DIFFRACTION98

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