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- PDB-9f8i: Crystal Structure of PhzA/B from Burkholderia cepacia R18194 in c... -

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Basic information

Entry
Database: PDB / ID: 9f8i
TitleCrystal Structure of PhzA/B from Burkholderia cepacia R18194 in complex with (4-Chlorophenyl)[6-hydroxy-2-(4-hydroxyphenyl)benzo[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: 1.39 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
C: Phenazine biosynthesis protein A/B
D: Phenazine biosynthesis protein A/B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,14014
Polymers86,1244
Non-polymers2,01610
Water13,349741
1
A: Phenazine biosynthesis protein A/B
B: Phenazine biosynthesis protein A/B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0707
Polymers43,0622
Non-polymers1,0085
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-21 kcal/mol
Surface area13510 Å2
MethodPISA
2
C: Phenazine biosynthesis protein A/B
D: Phenazine biosynthesis protein A/B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0707
Polymers43,0622
Non-polymers1,0085
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-22 kcal/mol
Surface area13490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.855, 68.157, 82.807
Angle α, β, γ (deg.)90.00, 90.15, 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.: 4
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-A1IAE / (4-chlorophenyl)-[2-(4-hydroxyphenyl)-6-oxidanyl-1-benzothiophen-3-yl]methanone / (4-Chlorophenyl)[6-hydroxy-2-(4-hydroxyphenyl)benzo[b]thiophen-3-yl]methanone


Mass: 380.844 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H13ClO3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 741 / 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: 2.33 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 18.3% (w/v) PEG 3350, 0.1 M Bis-TRIS pH 6.56, 0.133 M lithium 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: 1.39→19.24 Å / Num. obs: 152416 / % possible obs: 98.9 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.024 / Rrim(I) all: 0.065 / Net I/σ(I): 14.3
Reflection shellResolution: 1.39→1.41 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 7496 / CC1/2: 0.948 / Rpim(I) all: 0.167 / Rrim(I) all: 0.439

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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: 1.39→19.14 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.156 7276 4.78 %
Rwork0.1292 --
obs0.1305 152234 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.446 Å2
Refinement stepCycle: LAST / Resolution: 1.39→19.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4980 0 136 741 5857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085350
X-RAY DIFFRACTIONf_angle_d0.9177257
X-RAY DIFFRACTIONf_dihedral_angle_d14.1132008
X-RAY DIFFRACTIONf_chiral_restr0.075701
X-RAY DIFFRACTIONf_plane_restr0.012996
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.40.20242450.15664704X-RAY DIFFRACTION97
1.4-1.420.19682430.14194808X-RAY DIFFRACTION99
1.42-1.440.16232830.13474789X-RAY DIFFRACTION99
1.44-1.460.18362100.1364843X-RAY DIFFRACTION99
1.46-1.480.17242660.13874785X-RAY DIFFRACTION99
1.48-1.50.17112280.13164823X-RAY DIFFRACTION98
1.5-1.520.16322210.12894813X-RAY DIFFRACTION98
1.52-1.540.15582580.12294788X-RAY DIFFRACTION99
1.54-1.560.15032370.12464820X-RAY DIFFRACTION98
1.56-1.590.17912350.12334815X-RAY DIFFRACTION99
1.59-1.620.14682370.11554706X-RAY DIFFRACTION97
1.62-1.650.14113020.11384746X-RAY DIFFRACTION99
1.65-1.680.14282650.10944863X-RAY DIFFRACTION99
1.68-1.710.13231800.10784885X-RAY DIFFRACTION99
1.71-1.750.13892200.11044850X-RAY DIFFRACTION99
1.75-1.790.13552960.11314850X-RAY DIFFRACTION99
1.79-1.840.17282440.11654795X-RAY DIFFRACTION99
1.84-1.880.14172150.11614892X-RAY DIFFRACTION99
1.88-1.940.12622430.11274845X-RAY DIFFRACTION99
1.94-20.14352290.11784814X-RAY DIFFRACTION99
2-2.070.14892040.12414857X-RAY DIFFRACTION98
2.07-2.160.15412830.12684828X-RAY DIFFRACTION99
2.16-2.250.15152450.12254698X-RAY DIFFRACTION97
2.25-2.370.1372350.11964912X-RAY DIFFRACTION100
2.37-2.520.1483220.12244826X-RAY DIFFRACTION100
2.52-2.720.14893030.13064856X-RAY DIFFRACTION100
2.72-2.990.15321800.13254977X-RAY DIFFRACTION100
2.99-3.420.14752200.1394935X-RAY DIFFRACTION99
3.42-4.30.17742150.13564818X-RAY DIFFRACTION97
4.3-19.140.20262120.16185017X-RAY DIFFRACTION99

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