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- PDB-8qbh: AntI in complex with 1-Naphthol -

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Basic information

Entry
Database: PDB / ID: 8qbh
TitleAntI in complex with 1-Naphthol
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 / 1-NAPHTHOL / 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: 2.05 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 24, 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)46,1712
Polymers46,0261
Non-polymers1441
Water1,76598
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)92,3414
Polymers92,0532
Non-polymers2882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557x,-y,-z+21
Buried area3970 Å2
ΔGint-19 kcal/mol
Surface area26730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.940, 154.730, 92.090
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-536-

HOH

21A-598-

HOH

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Components

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


Mass: 46026.445 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-1NP / 1-NAPHTHOL / naphthalen-1-ol


Mass: 144.170 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.16 Å3/Da / Density % sol: 43.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 100 mM HEPES pH 7.9, 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: Aug 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 24440 / % possible obs: 95.8 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 17.29
Reflection shellResolution: 2.05→2.15 Å / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 3238

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→45.68 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.963 / SU B: 8.246 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2072 1221 5 %RANDOM
Rwork0.19164 ---
obs0.19242 23215 95.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.634 Å2
Baniso -1Baniso -2Baniso -3
1-36.38 Å20 Å20 Å2
2---18.83 Å2-0 Å2
3----17.56 Å2
Refinement stepCycle: 1 / Resolution: 2.05→45.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2993 0 11 98 3102
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0133098
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162818
X-RAY DIFFRACTIONr_angle_refined_deg1.141.624210
X-RAY DIFFRACTIONr_angle_other_deg1.071.5716473
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.485382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.72423.208159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26215495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2821512
X-RAY DIFFRACTIONr_chiral_restr0.0370.2394
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023551
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02759
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_it0.913.8571513
X-RAY DIFFRACTIONr_mcbond_other0.913.8571512
X-RAY DIFFRACTIONr_mcangle_it1.3225.7851891
X-RAY DIFFRACTIONr_mcangle_other1.3225.7861892
X-RAY DIFFRACTIONr_scbond_it0.7663.9511585
X-RAY DIFFRACTIONr_scbond_other0.7653.9521586
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0885.8972317
X-RAY DIFFRACTIONr_long_range_B_refined2.10644.983519
X-RAY DIFFRACTIONr_long_range_B_other2.10544.9783520
X-RAY DIFFRACTIONr_rigid_bond_restr0.22435912
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 89 -
Rwork0.215 1693 -
obs--96.27 %
Refinement TLS params.Method: refined / Origin x: 12.9955 Å / Origin y: 17.0662 Å / Origin z: 95.064 Å
111213212223313233
T0.0978 Å2-0.0261 Å20.0487 Å2-0.0092 Å2-0.0181 Å2--0.0521 Å2
L1.1684 °20.2407 °2-0.2629 °2-2.1031 °2-0.3009 °2--2.8038 °2
S0.0983 Å °-0.036 Å °0.195 Å °-0.0622 Å °0.0164 Å °-0.0466 Å °-0.4398 Å °0.0792 Å °-0.1147 Å °

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