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- PDB-4c6v: Crystal structure of M. tuberculosis KasA in complex with TLM5 (S... -

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Basic information

Entry
Database: PDB / ID: 4c6v
TitleCrystal structure of M. tuberculosis KasA in complex with TLM5 (Soak for 5 min)
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: 2.7 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 / 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)46,1604
Polymers45,8211
Non-polymers3393
Water1,58588
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)92,3208
Polymers91,6412
Non-polymers6796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area7090 Å2
ΔGint-47.2 kcal/mol
Surface area26290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.230, 77.230, 146.851
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.92 Å3/Da / Density % sol: 57.86 % / 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: BESSY / Beamline: 14.1 / Wavelength: 0.9184
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.7→49.44 Å / Num. obs: 14534 / % possible obs: 100 % / Observed criterion σ(I): 6 / Redundancy: 5.4 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.2
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

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

2wge


Resolution: 2.7→66.88 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.891 / SU B: 25.395 / SU ML: 0.231 / Cross valid method: THROUGHOUT / ESU R: 0.785 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24217 729 5 %RANDOM
Rwork0.17643 ---
obs0.17969 13755 99.86 %-
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: 42.271 Å2
Baniso -1Baniso -2Baniso -3
1-1.67 Å20.84 Å20 Å2
2--1.67 Å20 Å2
3----2.51 Å2
Refinement stepCycle: LAST / Resolution: 2.7→66.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3030 0 21 88 3139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223109
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.974225
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2555414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.4523.415123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.1515471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9391524
X-RAY DIFFRACTIONr_chiral_restr0.0980.2471
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212425
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_it0.6841.52052
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.29923262
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.03631057
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3664.5963
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: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 52 -
Rwork0.257 1015 -
obs--100 %
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)
10.985-0.03270.2753.4480.2711.3810.06520.0766-0.4201-0.15510.03540.36620.4094-0.0819-0.10060.292-0.01940.03280.2099-0.05910.263938.0363-15.791934.4034
23.5427-3.1499-1.139810.03560.530914.5844-0.1466-0.4698-0.10190.84950.13740.74410.8763-0.7640.00930.1847-0.12870.13710.2192-0.08810.147528.6376-19.373249.9745
312.3393-5.9134-0.00655.73562.25445.99190.34730.0768-0.47810.6009-0.50430.19691.0494-0.18310.15710.3054-0.11060.05190.0845-0.00090.096742.4074-20.959250.5397
45.8857-4.1505-1.32383.6897-0.47233.0570.09470.3667-0.02-0.0595-0.20180.0350.2355-0.24730.10710.3509-0.11580.07090.116-0.1490.31832.9132-7.978156.13
53.6802-1.50421.04732.5768-2.06646.60230.04020.0790.29810.1067-0.1915-0.23570.19470.02650.15140.14340.0136-0.00240.03250.0080.071147.8543-4.840446.7357
62.115-0.93091.24732.761-0.96512.65590.19560.028-0.1938-0.26210.02360.21440.1398-0.1547-0.21920.11450.02120.00990.0481-0.00440.060337.7081-8.445433.5658
72.7799-5.55811.281811.4615-1.236611.84280.08290.32410.37760.0401-0.4682-1.0581.21411.04450.38540.18460.1255-0.01370.2221-0.00910.617760.3332-20.083844.8292
80.4597-0.59460.6872.55660.15371.65970.08730.10790.0461-0.4898-0.0271-0.2906-0.13560.1807-0.06020.18940.0470.09990.10060.00030.063648.8976-4.955529.219
91.9463-0.1433-0.2832.94351.94411.8110.20920.2670.0904-0.71970.0138-0.4895-0.38110.131-0.2230.25670.07020.14320.12170.03340.106550.1731-9.505525.5366
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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