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- PDB-4c6u: Crystal structure of M. tuberculosis KasA in complex with TLM5 -

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Basic information

Entry
Database: PDB / ID: 4c6u
TitleCrystal structure of M. tuberculosis KasA in complex with TLM5
Components3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1
KeywordsTRANSFERASE / KAS ENZYME / TYPE 2 FATTY ACID BIOSYNTHESIS / MYCOLIC ACID SYNTHESIS / THIOLACTOMYCIN
Function / homologyThiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / : / Chem-TLG / :
Function and homology information
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSchiebel, J. / Kapilashrami, K. / Fekete, A. / Bommineni, G.R. / Schaefer, C.M. / Mueller, M.J. / Tonge, P.J. / Kisker, C.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural Basis for the Recognition of Mycolic Acid Precursors by Kasa, a Condensing Enzyme and Drug Target from Mycobacterium Tuberculosis
Authors: Schiebel, J. / Kapilashrami, K. / Fekete, A. / Bommineni, G.R. / Schaefer, C.M. / Mueller, M.J. / Tonge, P.J. / Kisker, C.
History
DepositionSep 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references
Revision 1.2Oct 23, 2013Group: Database references
Revision 1.3Dec 11, 2013Group: Database references
Revision 1.4Dec 20, 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 / pdbx_struct_special_symmetry / 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 / _pdbx_struct_conn_angle.value / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3207
Polymers45,8211
Non-polymers4996
Water2,036113
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)92,63914
Polymers91,6412
Non-polymers99812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area7660 Å2
ΔGint-53.8 kcal/mol
Surface area26740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.582, 77.582, 147.650
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2052-

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


Mass: 45820.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PFPCA1 / Production host: MYCOBACTERIUM SMEGMATIS (bacteria) / Strain (production host): MC2155
References: UniProt: I6Y8T4, beta-ketoacyl-[acyl-carrier-protein] synthase I

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Non-polymers , 5 types, 119 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-TLG / (5R)-3-acetyl-4-hydroxy-5-methyl-5-[(1Z)-2-methylbuta-1,3-dien-1-yl]thiophen-2(5H)-one


Mass: 238.303 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14O3S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.96 Å3/Da / Density % sol: 58.47 % / Description: NONE
Crystal growpH: 9.5
Details: 10% PEG 3350, 0.2 M K/NA-TARTRATE, 1.5 MM TCEP, pH 9.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.4→49.22 Å / Num. obs: 20763 / % possible obs: 99.8 % / Observed criterion σ(I): 6 / Redundancy: 7.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.9
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 6 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WGE

2wge


Resolution: 2.4→67.19 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 14.493 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.27 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21639 1061 5.1 %RANDOM
Rwork0.16385 ---
obs0.16656 19647 99.68 %-
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: 52.186 Å2
Baniso -1Baniso -2Baniso -3
1-1.67 Å20.83 Å20 Å2
2--1.67 Å20 Å2
3----2.5 Å2
Refinement stepCycle: LAST / Resolution: 2.4→67.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3024 0 30 113 3167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223115
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.9714230
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1475415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97523.415123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.75315473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3651524
X-RAY DIFFRACTIONr_chiral_restr0.080.2471
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212425
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2821.52050
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.21323260
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.77831065
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.6454.5969
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: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 87 -
Rwork0.234 1399 -
obs--99.73 %
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)
12.531.3266-0.36941.16180.0181.24860.0473-0.1887-0.3730.0004-0.01240.04960.2334-0.1613-0.03490.2367-0.05570.00210.2990.01510.2922-33.004325.3451-34.5644
27.36970.75051.1164.66030.488813.4820.16060.6157-0.5006-0.71790.1142-0.21580.7609-0.5952-0.27480.31-0.06630.11020.106-0.07710.1589-30.980315.0491-50.0749
314.4301-5.44771.82715.9592-1.75331.9113-0.33380.0468-0.3966-0.77450.30430.37360.506-0.67990.02950.314-0.20050.04550.2848-0.03430.1384-39.464526.389-50.8537
44.8837-2.28780.04361.50930.61221.3096-0.10980.0137-0.0588-0.01040.0224-0.02520.2223-0.1850.08730.3032-0.16510.10940.1740.00030.2828-23.674124.8164-56.6108
51.8525-0.07850.1772.5141-0.6034.14-0.188-0.0510.2650.09510.10290.1374-0.15280.01910.08520.0508-0.0418-0.00740.1211-0.00640.0951-28.225739.2582-47.0424
62.8149-0.12940.85461.2741-0.21611.72480.0852-0.2776-0.22140.02920.06380.04510.0782-0.0025-0.1490.0183-0.03160.01190.116-0.02790.0566-26.367828.5828-33.6365
710.73792.44925.86071.83212.43787.0623-0.25170.27550.098-0.1440.32730.482-0.661-0.4938-0.07560.12560.11780.00990.39960.15750.3975-47.748842.3705-45.2385
82.58660.6485-0.2170.6737-0.48411.7860.093-0.41010.20070.1185-0.06460.1464-0.13070.0533-0.02830.0392-0.02450.03030.1928-0.0650.0521-28.906740.0473-29.434
92.27390.5218-1.53011.2837-0.39572.36010.1598-0.52870.31210.1985-0.08610.118-0.18880.1918-0.07370.0502-0.02940.03290.2339-0.10780.0736-33.586338.9105-25.7137
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 63
2X-RAY DIFFRACTION2A64 - 82
3X-RAY DIFFRACTION3A83 - 102
4X-RAY DIFFRACTION4A103 - 160
5X-RAY DIFFRACTION5A161 - 183
6X-RAY DIFFRACTION6A184 - 251
7X-RAY DIFFRACTION7A252 - 266
8X-RAY DIFFRACTION8A267 - 372
9X-RAY DIFFRACTION9A373 - 416

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