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- PDB-9glf: Anthraquinone Pigment Production Regulated by Cinnamic Acid -

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Basic information

Entry
Database: PDB / ID: 9glf
TitleAnthraquinone Pigment Production Regulated by Cinnamic Acid
ComponentsAntI
KeywordsLYASE / Pigment Biosynthesis / Type II Polyketide Synthase System / Competitive Inhibition / Regulation
Function / homologyEsterase FrsA-like / Esterase FrsA-like / Alpha/Beta hydrolase fold / ACETATE ION / DI(HYDROXYETHYL)ETHER / PHENYLETHYLENECARBOXYLIC ACID / 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: 1.4 Å
AuthorsSu, L. / Schmalhofer, M. / Grammbitter, G.L.C. / Paczia, N. / Glatter, T. / Groll, M. / Bode, H.B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1309 Germany
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: The Isopropylstilbene Precursor Cinnamic Acid Inhibits Anthraquinone Pigment Production by Targeting AntI.
Authors: Su, L. / Schmalhofer, M. / Grammbitter, G.L.C. / Paczia, N. / Glatter, T. / Groll, M. / Bode, H.B.
History
DepositionAug 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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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)46,3978
Polymers45,7811
Non-polymers6167
Water4,756264
1
A: AntI
hetero molecules

A: AntI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,79316
Polymers91,5622
Non-polymers1,23114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557x,-y,-z+21
Buried area5840 Å2
ΔGint-62 kcal/mol
Surface area27880 Å2
Unit cell
Length a, b, c (Å)54.380, 154.460, 91.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-650-

HOH

21A-760-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7MZT8

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Non-polymers , 7 types, 271 molecules

#2: Chemical ChemComp-TCA / PHENYLETHYLENECARBOXYLIC ACID


Mass: 148.159 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


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


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


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.09 Å3/Da / Density % sol: 41.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6 / Details: 0.1 M NaAc, 0.1M HEPES, 25% 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: Feb 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 74543 / % possible obs: 98.4 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 20.2
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 2 / Num. unique obs: 13812 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→30 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.998 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1809 3727 5 %RANDOM
Rwork0.1472 ---
obs0.1488 70809 98.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.67 Å2 / Biso mean: 25.737 Å2 / Biso min: 14.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.83 Å2
Refinement stepCycle: final / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3049 0 41 265 3355
Biso mean--40.77 37.66 -
Num. residues----377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0133211
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162984
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.6284339
X-RAY DIFFRACTIONr_angle_other_deg1.4031.5796882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9035388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.24422.965172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.41815545
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6151515
X-RAY DIFFRACTIONr_chiral_restr0.0750.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023639
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02783
X-RAY DIFFRACTIONr_rigid_bond_restr1.39436185
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.46 274 -
Rwork0.469 5195 -
all-5469 -
obs--98.33 %

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