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- PDB-8qd5: AntI Ser245DHA (PSF) -

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Basic information

Entry
Database: PDB / ID: 8qd5
TitleAntI Ser245DHA (PSF)
ComponentsPhotorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17
KeywordsLYASE / Natural Product Biosynthesis / Polyketide Synthase System / alpha / beta-Hydrolase Fold / Polyketide Shortening / Retro Claisen Reaction
Function / homologyEsterase FrsA-like / Esterase FrsA-like / Alpha/Beta hydrolase fold / ACETATE ION / Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17
Function and homology information
Biological speciesPhotorhabdus laumondii subsp. laumondii TTO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSchmalhofer, M. / Vagstad, A.L. / Zhou, Q. / Bode, H.B. / Groll, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB 1309 - 325871075 Germany
CitationJournal: Adv Sci / Year: 2024
Title: Polyketide Trimming Shapes Dihydroxynaphthalene-Melanin and Anthraquinone Pigments.
Authors: Schmalhofer, M. / Vagstad, A.L. / Zhou, Q. / Bode, H.B. / Groll, M.
History
DepositionAug 28, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 19, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3475
Polymers46,0081
Non-polymers3384
Water5,314295
1
A: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17
hetero molecules

A: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,69410
Polymers92,0172
Non-polymers6778
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557x,-y,-z+21
Buried area5270 Å2
ΔGint-36 kcal/mol
Surface area27220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.570, 154.600, 91.460
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-509-

HOH

21A-602-

HOH

31A-787-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17


Mass: 46008.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus laumondii subsp. laumondii TTO1 (bacteria)
Gene: plu4186 / Plasmid: pColaDUET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7MZT8

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Non-polymers , 5 types, 299 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.1 Å3/Da / Density % sol: 41.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 100 mM HEPES pH 7.1, 0.1 M NaAc pH 6.6, 24% 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: Mar 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 35748 / % possible obs: 98.4 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 18.2
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 5333 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→44.85 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 4.122 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19597 1787 5 %RANDOM
Rwork0.16157 ---
obs0.16332 33957 98.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.154 Å2
Baniso -1Baniso -2Baniso -3
1--3.92 Å20 Å20 Å2
2---19.8 Å2-0 Å2
3---23.73 Å2
Refinement stepCycle: 1 / Resolution: 1.8→44.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3005 0 22 295 3322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0133113
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162845
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.6234217
X-RAY DIFFRACTIONr_angle_other_deg1.1911.5736542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6965380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.24423.148162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.54215502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5131512
X-RAY DIFFRACTIONr_chiral_restr0.0530.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023549
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02751
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_it1.1232.241512
X-RAY DIFFRACTIONr_mcbond_other1.1052.2381510
X-RAY DIFFRACTIONr_mcangle_it1.4613.361888
X-RAY DIFFRACTIONr_mcangle_other1.4623.3611889
X-RAY DIFFRACTIONr_scbond_it1.1082.4141601
X-RAY DIFFRACTIONr_scbond_other1.1082.4151602
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4423.5562328
X-RAY DIFFRACTIONr_long_range_B_refined2.41927.8643659
X-RAY DIFFRACTIONr_long_range_B_other2.19727.0853586
X-RAY DIFFRACTIONr_rigid_bond_restr0.7735953
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 131 -
Rwork0.273 2486 -
obs--99.35 %
Refinement TLS params.Method: refined / Origin x: 13.1206 Å / Origin y: 17.2749 Å / Origin z: 94.2432 Å
111213212223313233
T0.0163 Å2-0.0064 Å2-0.0055 Å2-0.0868 Å2-0.0054 Å2--0.0236 Å2
L0.9917 °20.1375 °2-0.273 °2-1.312 °2-0.1385 °2--1.2909 °2
S-0.0148 Å °0.0088 Å °0.1427 Å °-0.0119 Å °0.0174 Å °-0.0245 Å °-0.1343 Å °0.0373 Å °-0.0026 Å °

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