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- PDB-2wge: Crystal structure of KasA of Mycobacterium tuberculosis with bound TLM -

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Basic information

Entry
Database: PDB / ID: 2wge
TitleCrystal structure of KasA of Mycobacterium tuberculosis with bound TLM
Components3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1
KeywordsTRANSFERASE / BETA KETOACYL SYNTHASE I THIOLACTOMYCIN / 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
ISOPROPYL ALCOHOL / 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: 1.8 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 / 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_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 / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,29811
Polymers43,3601
Non-polymers93810
Water5,062281
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)88,59622
Polymers86,7202
Non-polymers1,87620
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area7710 Å2
ΔGint-62.1 kcal/mol
Surface area32260 Å2
MethodPQS
Unit cell
Length a, b, c (Å)77.542, 77.542, 148.458
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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 SYNTHASE I / KAS 1 / BETA-KETOACYL-ACP SYNTHASE 1


Mass: 43359.980 Da / Num. of mol.: 1
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, 291 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: 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.: 1 / Source method: obtained synthetically / Formula: C11H14O2S
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 3.04 Å3/Da / Density % sol: 59.51 % / Description: NONE
Crystal growDetails: 2-PROPANOL NACL HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.79→50.06 Å / Num. obs: 48833 / % possible obs: 99 % / Redundancy: 6.7 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.1
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.45 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 7.5 / % possible all: 93.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALA(CCP4)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WGD

2wgd


Resolution: 1.8→49.81 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.014 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20129 2434 5 %RANDOM
Rwork0.16737 ---
obs0.16902 46350 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.381 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20.37 Å20 Å2
2--0.74 Å20 Å2
3----1.1 Å2
Refinement stepCycle: LAST / Resolution: 1.8→49.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3029 0 61 281 3371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223222
X-RAY DIFFRACTIONr_bond_other_d0.0020.022164
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.9794386
X-RAY DIFFRACTIONr_angle_other_deg0.97435280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1415440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.95923.615130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53515496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4711525
X-RAY DIFFRACTIONr_chiral_restr0.0880.2486
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023688
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02631
X-RAY DIFFRACTIONr_nbd_refined0.2160.2634
X-RAY DIFFRACTIONr_nbd_other0.1960.22344
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21570
X-RAY DIFFRACTIONr_nbtor_other0.0850.21591
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2211
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1140.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4710.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2790.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.781.52091
X-RAY DIFFRACTIONr_mcbond_other0.1991.5868
X-RAY DIFFRACTIONr_mcangle_it1.3823341
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.17131159
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.594.51033
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.839 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 137 -
Rwork0.206 3006 -
obs--87.02 %

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