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- PDB-5dz7: STRUCTURAL BASIS OF ACYL TRANSFER IN A TRANS-AT POLYKETIDE SYNTHASE -

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Basic information

Entry
Database: PDB / ID: 5dz7
TitleSTRUCTURAL BASIS OF ACYL TRANSFER IN A TRANS-AT POLYKETIDE SYNTHASE
ComponentsPolyketide biosynthesis protein PksE
KeywordsTRANSFERASE / ACYLTRANSFERASE
Function / homology
Function and homology information


nitronate monooxygenase activity / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / antibiotic biosynthetic process / fatty acid biosynthetic process / cytosol
Similarity search - Function
PfaD family protein / Nitronate monooxygenase / Nitronate monooxygenase / Malonyl CoA-acyl carrier protein transacylase, FabD-type / Malonyl-CoA ACP transacylase, ACP-binding / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase domain superfamily / Acyl transferase ...PfaD family protein / Nitronate monooxygenase / Nitronate monooxygenase / Malonyl CoA-acyl carrier protein transacylase, FabD-type / Malonyl-CoA ACP transacylase, ACP-binding / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Aldolase-type TIM barrel / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyketide biosynthesis protein PksE
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRace, P.R. / Till, M.
CitationJournal: To Be Published
Title: Structural Basis Of Acyl Transfer In A Trans-At Polyketide Synthase
Authors: Race, P.R. / Till, M.
History
DepositionSep 25, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyketide biosynthesis protein PksE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8895
Polymers34,5771
Non-polymers3124
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-5 kcal/mol
Surface area12090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.653, 54.546, 116.708
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Polyketide biosynthesis protein PksE / MALONYL COA-ACYL CARRIER PROTEIN TRANSACYLASE / MCT


Mass: 34577.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Gene: pksE, BSU17120 / Plasmid: PET28A / Production host: ESCHERICHIA COLI BL21 (bacteria)
References: UniProt: O34787, [acyl-carrier-protein] S-malonyltransferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 1.96 Å3/Da / Density % sol: 37.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 MM MES, 15-25% (W/V) POLYETHYLENE GLYCOL 6000, AND 200 MM LITHIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
PH range: 6-7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.5→19.91 Å / Num. obs: 17182 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Net I/σ(I): 9.6
Reflection shellResolution: 2.5→2.64 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
REFMAC5.6.0117refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→19.91 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.863 / SU B: 12.227 / SU ML: 0.264 / Cross valid method: THROUGHOUT / ESU R: 1.38 / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28 471 4.8 %RANDOM
Rwork0.192 ---
obs0.196 9431 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.36 Å20 Å20 Å2
2---1.38 Å20 Å2
3---3.74 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2181 0 19 75 2275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022240
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.9613027
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9775280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.75124.906106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1915372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1671510
X-RAY DIFFRACTIONr_chiral_restr0.1060.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211705
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 25 -
Rwork0.258 613 -
obs--99.53 %

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