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- PDB-3tzx: Crystal structure of a fragment containing the acyltransferase do... -

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Basic information

Entry
Database: PDB / ID: 3tzx
TitleCrystal structure of a fragment containing the acyltransferase domain of Pks13 from Mycobacterium tuberculosis in tetragonal apo form at 2.3 A
Components
  • 12-mer peptide
  • Polyketide synthase PKS13
KeywordsTRANSFERASE / Acyltransferase / Long fatty acid chain transferase / Acyl carrier protein
Function / homology
Function and homology information


polyketide synthase complex / fatty acid elongation, saturated fatty acid / mycolate cell wall layer assembly / mycolic acid biosynthetic process / DIM/DIP cell wall layer assembly / acyltransferase activity, transferring groups other than amino-acyl groups / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / peptidoglycan-based cell wall ...polyketide synthase complex / fatty acid elongation, saturated fatty acid / mycolate cell wall layer assembly / mycolic acid biosynthetic process / DIM/DIP cell wall layer assembly / acyltransferase activity, transferring groups other than amino-acyl groups / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / peptidoglycan-based cell wall / protein homooligomerization / plasma membrane / cytosol
Similarity search - Function
: / Malonyl-CoA ACP transacylase, ACP-binding / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Thioesterase / Thioesterase domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / : ...: / Malonyl-CoA ACP transacylase, ACP-binding / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Thioesterase / Thioesterase domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / 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 / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMycobacterium tuberculosis (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBergeret, F. / Pedelacq, J.D. / Mourey, L. / Bon, C.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Biochemical and structural study of the atypical acyltransferase domain from the mycobacterial polyketide synthase pks13
Authors: Bergeret, F. / Gavalda, S. / Chalut, C. / Malaga, W. / Quemard, A. / Pedelacq, J.D. / Daffe, M. / Guilhot, C. / Mourey, L. / Bon, C.
History
DepositionSep 28, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Polyketide synthase PKS13
B: Polyketide synthase PKS13
C: 12-mer peptide
D: 12-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,63712
Polymers108,8854
Non-polymers7538
Water6,323351
1
A: Polyketide synthase PKS13
D: 12-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6264
Polymers54,4422
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-9 kcal/mol
Surface area19370 Å2
MethodPISA
2
B: Polyketide synthase PKS13
C: 12-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0118
Polymers54,4422
Non-polymers5686
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-47 kcal/mol
Surface area19680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.560, 106.560, 258.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-133-

HOH

DetailsTHE HETERODIMER FORMED BETWEEN THE UNKNOWN PEPTIDE AND THE ACYLTRANSFERASE DOMAIN OF PKS13 HAS NO KNOWN FUNCTIONAL RELEVANCE FOR THE TIME BEING

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Components

#1: Protein Polyketide synthase PKS13 / Polyketide synthase


Mass: 53086.805 Da / Num. of mol.: 2 / Fragment: Acyltransferase domain, UNP residues 576-1062
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv3800c / Plasmid: pWM71, pET28aII / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS
References: UniProt: O53579, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Protein/peptide 12-mer peptide / Co-crystallized peptide


Mass: 1355.495 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: The author presume that this peptide comes from the Escherichia coli strain that was used to produce the recombinant protein.
Source: (natural) Escherichia coli (E. coli)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 3.37 Å3/Da / Density % sol: 63.51 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 1.7m ammonium sulfate, 15% glycerol, 1.7% PEG-400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.3→41.7 Å / Num. obs: 65097 / % possible obs: 96.9 % / Redundancy: 4.2 % / Biso Wilson estimate: 41.5 Å2 / Rsym value: 0.067
Reflection shellResolution: 2.3→2.4 Å / Mean I/σ(I) obs: 2.3 / Rsym value: 0.329 / % possible all: 83.4

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID: 2HG4

2hg4


Resolution: 2.3→41.12 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.914 / SU B: 6.6 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26047 3291 5.1 %RANDOM
Rwork0.20017 ---
all0.20319 61727 --
obs0.20319 61727 96.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.269 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å20 Å2
2--1.05 Å20 Å2
3----2.1 Å2
Refinement stepCycle: LAST / Resolution: 2.3→41.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7123 0 44 351 7518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0197317
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0681.9639950
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8835951
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.51723.792298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.301151130
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9911544
X-RAY DIFFRACTIONr_chiral_restr0.1320.21141
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215541
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 178 -
Rwork0.249 3463 -
obs--79.1 %

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