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- PDB-9f8q: Crystal Structure of PhzA/B from Burkholderia cepacia R18194 in c... -

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Basic information

Entry
Database: PDB / ID: 9f8q
TitleCrystal Structure of PhzA/B from Burkholderia cepacia R18194 in complex with [6-Hydroxy-2-(4-hydroxyphenyl)benzo[b]thiophen-3-yl](2-hydroxyphenyl)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 / : / Phenazine biosynthesis protein A/B
Function and homology information
Biological speciesBurkholderia lata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 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)44,0637
Polymers43,0622
Non-polymers1,0015
Water6,846380
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.968, 68.802, 54.059
Angle α, β, γ (deg.)90.00, 101.03, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-A1IAJ / (2-hydroxyphenyl)-[2-(4-hydroxyphenyl)-6-oxidanyl-1-benzothiophen-3-yl]methanone / [6-Hydroxy-2-(4-hydroxyphenyl)benzo[b]thiophen-3-yl](2-hydroxyphenyl)methanone


Mass: 362.398 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H14O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 2.35 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 23.3% (w/v) PEG 4000, 0.1 M Bis-TRIS pH 6.93, 8.33% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.34→53.06 Å / Num. obs: 86990 / % possible obs: 99 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.027 / Rrim(I) all: 0.073 / Χ2: 0.7 / Net I/σ(I): 11.9 / Num. measured all: 594834
Reflection shellResolution: 1.34→1.41 Å / % possible obs: 98.3 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.45 / Num. measured all: 80631 / Num. unique obs: 12620 / CC1/2: 0.949 / Rpim(I) all: 0.19 / Rrim(I) all: 0.489 / Χ2: 0.37 / Net I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
PHENIXv1.20.1_4487refinement
XDSJun 30, 2023data reduction
Aimlessv0.7.9data scaling
PHASERv2.8.3phasing
autoPROCv1.0.5 (20211020)data processing
PDB_EXTRACTv4.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.34→53.06 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 14.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1515 4156 4.78 %
Rwork0.1287 --
obs0.1298 86925 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.61 Å2
Refinement stepCycle: LAST / Resolution: 1.34→53.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2530 0 70 380 2980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092918
X-RAY DIFFRACTIONf_angle_d1.0243975
X-RAY DIFFRACTIONf_dihedral_angle_d14.8071080
X-RAY DIFFRACTIONf_chiral_restr0.089372
X-RAY DIFFRACTIONf_plane_restr0.013538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.350.29751300.29092702X-RAY DIFFRACTION95
1.35-1.370.30031520.25792688X-RAY DIFFRACTION99
1.37-1.380.23091370.22362762X-RAY DIFFRACTION99
1.38-1.40.22011380.19242738X-RAY DIFFRACTION99
1.4-1.420.21241290.16282777X-RAY DIFFRACTION99
1.42-1.440.16241310.14522743X-RAY DIFFRACTION99
1.44-1.460.17911380.13082809X-RAY DIFFRACTION99
1.46-1.480.15061630.11992706X-RAY DIFFRACTION99
1.48-1.50.14091350.11112761X-RAY DIFFRACTION99
1.5-1.530.14331160.10642770X-RAY DIFFRACTION99
1.53-1.560.15361360.10642773X-RAY DIFFRACTION100
1.56-1.580.17291250.10482755X-RAY DIFFRACTION99
1.58-1.610.13341360.112729X-RAY DIFFRACTION99
1.61-1.650.15061270.11242716X-RAY DIFFRACTION97
1.65-1.680.13931510.11892772X-RAY DIFFRACTION99
1.68-1.720.14011200.11872750X-RAY DIFFRACTION99
1.72-1.770.16121550.12142772X-RAY DIFFRACTION99
1.77-1.810.14911270.11512755X-RAY DIFFRACTION99
1.81-1.870.14271460.10862784X-RAY DIFFRACTION99
1.87-1.930.12651340.10332744X-RAY DIFFRACTION99
1.93-20.11141330.10432796X-RAY DIFFRACTION99
2-2.080.13981420.11182800X-RAY DIFFRACTION99
2.08-2.170.15221310.11372735X-RAY DIFFRACTION99
2.17-2.280.14031300.11032720X-RAY DIFFRACTION97
2.28-2.430.12771130.11052811X-RAY DIFFRACTION100
2.43-2.610.14131670.12092760X-RAY DIFFRACTION100
2.61-2.880.14211370.12912793X-RAY DIFFRACTION99
2.88-3.290.15611590.13432753X-RAY DIFFRACTION99
3.29-4.150.12861740.12722765X-RAY DIFFRACTION98
4.15-53.060.19541440.16332830X-RAY DIFFRACTION99

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