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

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Basic information

Entry
Database: PDB / ID: 3tzw
TitleCrystal structure of a fragment containing the acyltransferase domain of Pks13 from Mycobacterium tuberculosis in the orthorhombic apoform at 2.6 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 / acyltransferase activity, transferring groups other than amino-acyl groups / 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 / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Acyl transferase domain superfamily / Acyl transferase ...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 / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / 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 / 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: 2.6 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 / 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
D: 12-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,32913
Polymers54,4422
Non-polymers88711
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-87 kcal/mol
Surface area19920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.659, 119.806, 50.162
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
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.: 1 / 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: pET28aII, pWM71 / 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.: 1 / 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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 Å3/Da / Density % sol: 58.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.25
Details: 0.1M KH2PO4/K2HPO4, 1.3M ammonium sulfate, 10mM malonate, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 2.6→45 Å / Num. all: 20741 / Num. obs: 20741 / % possible obs: 99.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 43 Å2 / Rsym value: 0.106
Reflection shellResolution: 2.6→2.7 Å / Mean I/σ(I) obs: 1.6 / Rsym value: 0.368 / % possible all: 99.9

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 2HG4

2hg4


Resolution: 2.6→42.57 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.872 / SU B: 9.026 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26392 1016 4.9 %RANDOM
Rwork0.18671 ---
all0.19036 19692 --
obs0.19036 19692 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.284 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å20 Å2-0 Å2
2---1.1 Å20 Å2
3---2.26 Å2
Refinement stepCycle: LAST / Resolution: 2.6→42.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3527 0 50 145 3722
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0213654
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1471.9674967
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3735477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.92123.688141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.55215549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8451520
X-RAY DIFFRACTIONr_chiral_restr0.1390.2568
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212743
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_it1.1411.52373
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.11123774
X-RAY DIFFRACTIONr_scbond_it3.22431281
X-RAY DIFFRACTIONr_scangle_it5.2224.51193
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 79 -
Rwork0.272 1404 -
obs--99.66 %

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