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- PDB-8qd6: AntI Ser245DHA (PMSF) -

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Basic information

Entry
Database: PDB / ID: 8qd6
TitleAntI Ser245DHA (PMSF)
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: 1.7 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)46,2854
Polymers46,0081
Non-polymers2763
Water4,107228
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)92,5698
Polymers92,0172
Non-polymers5536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557x,-y,-z+21
Buried area4710 Å2
ΔGint-43 kcal/mol
Surface area27300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.720, 154.970, 91.370
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-605-

HOH

21A-651-

HOH

31A-725-

HOH

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Components

#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
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


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


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


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
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: 2.11 Å3/Da / Density % sol: 41.57 %
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: 1.7→50 Å / Num. obs: 42427 / % possible obs: 98.3 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 15.6
Reflection shellResolution: 1.7→1.8 Å / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 6613 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→44.93 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.967 / SU B: 3.02 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18826 2121 5 %RANDOM
Rwork0.16667 ---
obs0.16776 40299 98.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.435 Å2
Baniso -1Baniso -2Baniso -3
1-19.54 Å20 Å20 Å2
2---22.49 Å2-0 Å2
3---2.95 Å2
Refinement stepCycle: 1 / Resolution: 1.7→44.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3000 0 18 228 3246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0133104
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162850
X-RAY DIFFRACTIONr_angle_refined_deg1.1781.6214207
X-RAY DIFFRACTIONr_angle_other_deg1.1861.5736551
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6015380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.93923.125160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.25315503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8151512
X-RAY DIFFRACTIONr_chiral_restr0.0530.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023539
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02749
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_it1.0112.2651512
X-RAY DIFFRACTIONr_mcbond_other1.0042.2641510
X-RAY DIFFRACTIONr_mcangle_it1.3813.4011888
X-RAY DIFFRACTIONr_mcangle_other1.3813.4021889
X-RAY DIFFRACTIONr_scbond_it0.9842.4191592
X-RAY DIFFRACTIONr_scbond_other0.9842.421593
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2943.5722318
X-RAY DIFFRACTIONr_long_range_B_refined2.04427.3253555
X-RAY DIFFRACTIONr_long_range_B_other1.9526.8683511
X-RAY DIFFRACTIONr_rigid_bond_restr0.49835949
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 155 -
Rwork0.242 2948 -
obs--98.66 %
Refinement TLS params.Method: refined / Origin x: 13.01 Å / Origin y: 17.2503 Å / Origin z: 94.2247 Å
111213212223313233
T0.0198 Å2-0.0086 Å20.0018 Å2-0.0273 Å2-0.0119 Å2--0.0261 Å2
L1.0953 °20.1746 °2-0.3259 °2-1.6282 °2-0.1986 °2--1.7305 °2
S0.0094 Å °-0.0111 Å °0.1424 Å °-0.0113 Å °0.0226 Å °-0.0563 Å °-0.1797 Å °0.0698 Å °-0.032 Å °

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