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- PDB-9f8k: Crystal Structure of PhzA/B from Burkholderia cepacia R18194 in c... -

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Basic information

Entry
Database: PDB / ID: 9f8k
TitleCrystal Structure of PhzA/B from Burkholderia cepacia R18194 in complex with [6-Hydroxy-2-(4-hydroxyphenyl)benzo[b]thiophen-3-yl](3-isopropylphenyl)methanone
ComponentsPhenazine biosynthesis protein A/B
KeywordsBIOSYNTHETIC PROTEIN / pyocyanin / phenazine biosynthesis / virulence / inhibitor / ketosteroid-isomerase / cocrystal / PhzA/B / Burkholderia cepacia
Function / homologyPhenazine biosynthesis protein A/B / Phenazine biosynthesis protein A/B / antibiotic biosynthetic process / NTF2-like domain superfamily / : / ACETATE ION / Phenazine biosynthesis protein A/B
Function and homology information
Biological speciesBurkholderia lata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsThiemann, M. / Zimmermann, M. / Kunick, C. / Blankenfeldt, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2025
Title: From Bones to Bugs: Structure-Based Development of Raloxifene-Derived Pathoblockers That Inhibit Pyocyanin Production in Pseudomonas aeruginosa.
Authors: Thiemann, M. / Zimmermann, M. / Diederich, C. / Zhan, H. / Lebedev, M. / Pletz, J. / Baumgarten, J. / Handke, M. / Musken, M. / Breinbauer, R. / Krasteva-Christ, G. / Zanin, E. / Empting, M. ...Authors: Thiemann, M. / Zimmermann, M. / Diederich, C. / Zhan, H. / Lebedev, M. / Pletz, J. / Baumgarten, J. / Handke, M. / Musken, M. / Breinbauer, R. / Krasteva-Christ, G. / Zanin, E. / Empting, M. / Schiedel, M. / Kunick, C. / Blankenfeldt, W.
History
DepositionMay 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phenazine biosynthesis protein A/B
B: Phenazine biosynthesis protein A/B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8788
Polymers43,0622
Non-polymers8166
Water6,738374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-26 kcal/mol
Surface area13770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.363, 79.303, 64.064
Angle α, β, γ (deg.)90.00, 98.41, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-485-

HOH

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Components

#1: Protein Phenazine biosynthesis protein A/B


Mass: 21531.025 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia lata (bacteria) / Gene: Bcep18194_B1568 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q396C9
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-A1IAH / [2-(4-hydroxyphenyl)-6-oxidanyl-1-benzothiophen-3-yl]-(3-propan-2-ylphenyl)methanone / [6-Hydroxy-2-(4-hydroxyphenyl)benzo[b]thiophen-3-yl](3-isopropylphenyl)methanone


Mass: 388.479 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H20O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / Source method: isolated from a natural source / Formula: H2O
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: 2.14 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25% (w/v) PEG 3350, 0.1 M Bis-TRIS pH 6.37, 0.122 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.57→52.73 Å / Num. obs: 48015 / % possible obs: 96.9 % / Redundancy: 4.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.028 / Rrim(I) all: 0.06 / Χ2: 0.75 / Net I/σ(I): 12.8 / Num. measured all: 209361
Reflection shellResolution: 1.57→1.59 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 6632 / CC1/2: 0.775 / Rpim(I) all: 0.287 / Rrim(I) all: 0.571

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Processing

Software
NameVersionClassification
XDSJun 30, 2023data reduction
Aimlessv0.7.9data scaling
PHENIXv1.20.1-4487refinement
PHASERv2.8.3phasing
autoPROCv1.0.5 (20221121)data processing
PDB_EXTRACTv4.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→42.9 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 16.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1749 2412 5.02 %
Rwork0.1527 --
obs0.1538 48009 96.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.075 Å2
Refinement stepCycle: LAST / Resolution: 1.57→42.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2518 0 56 374 2948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062720
X-RAY DIFFRACTIONf_angle_d0.9453690
X-RAY DIFFRACTIONf_dihedral_angle_d15.078995
X-RAY DIFFRACTIONf_chiral_restr0.054353
X-RAY DIFFRACTIONf_plane_restr0.009495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.60.22981190.20442152X-RAY DIFFRACTION79
1.6-1.630.21641250.19182485X-RAY DIFFRACTION90
1.63-1.670.2231670.18322647X-RAY DIFFRACTION97
1.67-1.710.21611340.18782722X-RAY DIFFRACTION97
1.71-1.760.19821600.17662687X-RAY DIFFRACTION98
1.76-1.810.20391450.16712699X-RAY DIFFRACTION98
1.81-1.870.1831450.15752701X-RAY DIFFRACTION98
1.87-1.940.17061360.1542781X-RAY DIFFRACTION99
1.94-2.010.19591410.15642654X-RAY DIFFRACTION97
2.01-2.10.16721480.15612734X-RAY DIFFRACTION98
2.1-2.220.17021640.152745X-RAY DIFFRACTION99
2.22-2.350.161240.14512748X-RAY DIFFRACTION99
2.35-2.540.1891320.14642797X-RAY DIFFRACTION99
2.54-2.790.1711440.15232730X-RAY DIFFRACTION99
2.79-3.190.17521360.14612726X-RAY DIFFRACTION98
3.19-4.020.16211310.13512798X-RAY DIFFRACTION100
4.02-42.90.16021610.15622791X-RAY DIFFRACTION98

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