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- PDB-9f8s: Crystal Structure of PhzA/B from Burkholderia cepacia R18194 in c... -

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Basic information

Entry
Database: PDB / ID: 9f8s
TitleCrystal Structure of PhzA/B from Burkholderia cepacia R18194 in complex with (4-Chlorophenyl)[6-hydroxy-2-phenylbenzo[b]thiophen-3-yl]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: 1.69 Å
AuthorsZimmermann, M. / Thiemann, 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)44,0687
Polymers43,0622
Non-polymers1,0065
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-21 kcal/mol
Surface area13800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.018, 68.900, 54.082
Angle α, β, γ (deg.)90.00, 100.31, 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-A1IAM / (4-chlorophenyl)-(6-oxidanyl-2-phenyl-1-benzothiophen-3-yl)methanone / (4-Chlorophenyl)[6-hydroxy-2-phenylbenzo[b]thiophen-3-yl]methanone


Mass: 364.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H13ClO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25% (w/v) PEG 3350, 0.1M Bis-TRIS pH 5.99, 0.15 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0331 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0331 Å / Relative weight: 1
ReflectionResolution: 1.69→53.15 Å / Num. obs: 43245 / % possible obs: 98.2 % / Redundancy: 7.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.049 / Rrim(I) all: 0.133 / Net I/σ(I): 9.2
Reflection shellResolution: 1.69→1.72 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.018 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2094 / CC1/2: 0.885 / Rpim(I) all: 0.421 / Rrim(I) all: 1.103

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Processing

Software
NameVersionClassification
XDSJun 30, 2023data reduction
Aimlessv0.7.15data scaling
PHASERv2.8.3phasing
PHENIXv1.20.1-4487refinement
autoPROCv1.0.5 (20240123)data processing
PDB_EXTRACTv4.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→53.15 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 19.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1889 2141 4.95 %
Rwork0.1671 --
obs0.1682 43215 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.963 Å2
Refinement stepCycle: LAST / Resolution: 1.69→53.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2475 0 68 257 2800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052663
X-RAY DIFFRACTIONf_angle_d0.7633615
X-RAY DIFFRACTIONf_dihedral_angle_d14.434999
X-RAY DIFFRACTIONf_chiral_restr0.052350
X-RAY DIFFRACTIONf_plane_restr0.009501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.720.31771430.23782667X-RAY DIFFRACTION97
1.72-1.770.24591220.22512613X-RAY DIFFRACTION93
1.77-1.820.24031360.18322741X-RAY DIFFRACTION99
1.82-1.870.20781680.17542744X-RAY DIFFRACTION99
1.87-1.930.18761540.16832738X-RAY DIFFRACTION99
1.93-20.21491270.16982754X-RAY DIFFRACTION99
2-2.080.2121390.17412766X-RAY DIFFRACTION99
2.08-2.170.1891110.16042769X-RAY DIFFRACTION99
2.17-2.290.19931480.15692745X-RAY DIFFRACTION99
2.29-2.430.19161590.15372661X-RAY DIFFRACTION96
2.43-2.620.16781320.15862694X-RAY DIFFRACTION97
2.62-2.880.16291520.16252802X-RAY DIFFRACTION100
2.88-3.30.17721680.1632770X-RAY DIFFRACTION100
3.3-4.160.16241300.14422829X-RAY DIFFRACTION99
4.16-53.150.18981520.18442781X-RAY DIFFRACTION98

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