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- PDB-6hxa: AntI from P. luminescens catalyses terminal polyketide shortening... -

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Basic information

Entry
Database: PDB / ID: 6hxa
TitleAntI from P. luminescens catalyses terminal polyketide shortening in the biosynthesis of anthraquinones
ComponentsAntI
KeywordsLYASE / Natural Product Biosynthesis / Type II Polyketide Synthase System / alpha / beta-Hydrolase Fold / Cascade Reaction / Retro Claisen Reaction / Dieckmann Condensation
Function / homologyEsterase FrsA-like / Esterase FrsA-like / Alpha/Beta hydrolase fold / TRIETHYLENE GLYCOL / Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17
Function and homology information
Biological speciesPhotorhabdus luminescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsZhou, Q. / Braeuer, A. / Grammbitter, G. / Schmalhofer, M. / Saura, P. / Adihou, H. / Kaila, V.R.I. / Groll, M. / Bode, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB749 Germany
CitationJournal: Chem Sci / Year: 2019
Title: Molecular mechanism of polyketide shortening in anthraquinone biosynthesis ofPhotorhabdus luminescens.
Authors: Zhou, Q. / Brauer, A. / Adihou, H. / Schmalhofer, M. / Saura, P. / Grammbitter, G.L.C. / Kaila, V.R.I. / Groll, M. / Bode, H.B.
History
DepositionOct 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: AntI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1263
Polymers45,7811
Non-polymers3442
Water3,279182
1
A: AntI
hetero molecules

A: AntI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,2516
Polymers91,5622
Non-polymers6894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557x,-y,-z+21
Buried area4510 Å2
ΔGint-14 kcal/mol
Surface area28100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.110, 154.340, 91.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-617-

HOH

21A-676-

HOH

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Components

#1: Protein AntI


Mass: 45781.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: plu4186 / Plasmid: pCOLA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7MZT8
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.08 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM HEPES, 0.1 M NaAc, 22% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 33019 / % possible obs: 99.7 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 18.9
Reflection shellResolution: 1.85→1.95 Å / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SeMet derivative; coordinates not deposited

Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 7.206 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.39 / ESU R Free: 0.126 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2044 1649 5 %RANDOM
Rwork0.16771 ---
obs0.16983 31340 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.114 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å2-0 Å20 Å2
2---4.11 Å2-0 Å2
3---3.75 Å2
Refinement stepCycle: 1 / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3039 0 23 182 3244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0143153
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172808
X-RAY DIFFRACTIONr_angle_refined_deg0.7891.6384259
X-RAY DIFFRACTIONr_angle_other_deg0.741.6476568
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.315376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.92123.214168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71215532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3241513
X-RAY DIFFRACTIONr_chiral_restr0.0390.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023512
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02644
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_it1.0393.4251501
X-RAY DIFFRACTIONr_mcbond_other1.0373.4241500
X-RAY DIFFRACTIONr_mcangle_it1.4955.1341875
X-RAY DIFFRACTIONr_mcangle_other1.4945.1361876
X-RAY DIFFRACTIONr_scbond_it1.0433.7081652
X-RAY DIFFRACTIONr_scbond_other1.0433.7081652
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3845.4552384
X-RAY DIFFRACTIONr_long_range_B_refined2.32539.9543655
X-RAY DIFFRACTIONr_long_range_B_other2.24639.7013623
X-RAY DIFFRACTIONr_rigid_bond_restr0.35235956
X-RAY DIFFRACTIONr_sphericity_free31.382585
X-RAY DIFFRACTIONr_sphericity_bonded18.33355976
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 120 -
Rwork0.289 2295 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 13.099 Å / Origin y: 17.1772 Å / Origin z: 94.0862 Å
111213212223313233
T0.0005 Å20.0004 Å20.0016 Å2-0.04 Å2-0.0003 Å2--0.0195 Å2
L0.1063 °20.0423 °20.0011 °2-0.0949 °2-0.0118 °2--0.0125 °2
S-0.0013 Å °-0.0016 Å °0.0199 Å °0.0003 Å °0.0017 Å °0.0085 Å °0.0015 Å °0.0058 Å °-0.0004 Å °

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