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- PDB-9f8m: Crystal Structure of PhzA/B from Burkholderia cepacia R18194 in c... -

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Basic information

Entry
Database: PDB / ID: 9f8m
TitleCrystal Structure of PhzA/B from Burkholderia cepacia R18194 in complex with [6-Hydroxy-2-(4-hydroxyphenyl)benzo[b]thiophen-3-yl][4-(propylamino)phenyl]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: 1.43 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)88,26114
Polymers86,1244
Non-polymers2,13710
Water10,719595
1
A: Phenazine biosynthesis protein A/B
B: Phenazine biosynthesis protein A/B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1457
Polymers43,0622
Non-polymers1,0835
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-24 kcal/mol
Surface area13700 Å2
MethodPISA
2
C: Phenazine biosynthesis protein A/B
D: Phenazine biosynthesis protein A/B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1157
Polymers43,0622
Non-polymers1,0535
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-21 kcal/mol
Surface area13600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.251, 68.392, 83.838
Angle α, β, γ (deg.)90.00, 90.20, 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.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-A1IAK / [2-(4-hydroxyphenyl)-6-oxidanyl-1-benzothiophen-3-yl]-[4-(propylamino)phenyl]methanone / [6-Hydroxy-2-(4-hydroxyphenyl)benzo[b]thiophen-3-yl][4-(propylamino)phenyl]methanone


Mass: 403.493 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H21NO3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 595 / 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: 50.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 28.3% (w/v) PEG monomethyl ether

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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: Dec 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.43→69.25 Å / Num. obs: 143300 / % possible obs: 98.9 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.019 / Rrim(I) all: 0.05 / Net I/σ(I): 14.2
Reflection shellResolution: 1.43→1.45 Å / Redundancy: 6 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 6657 / CC1/2: 0.947 / Rpim(I) all: 0.207 / Rrim(I) all: 0.516

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Processing

Software
NameVersionClassification
XDSFeb 5, 2021data reduction
Aimlessv0.7.7data scaling
PHASERv2.8.3phasing
PHENIXv1.20.1-4487refinement
autoPROCv1.0.5 (20211020)data processing
PDB_EXTRACTv4.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→48.66 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1867 7245 5.07 %
Rwork0.1571 --
obs0.1586 142907 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.135 Å2
Refinement stepCycle: LAST / Resolution: 1.43→48.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4999 0 150 595 5744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075381
X-RAY DIFFRACTIONf_angle_d0.9017292
X-RAY DIFFRACTIONf_dihedral_angle_d14.0142027
X-RAY DIFFRACTIONf_chiral_restr0.075691
X-RAY DIFFRACTIONf_plane_restr0.0111010
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.440.23232550.21334084X-RAY DIFFRACTION90
1.44-1.460.21892380.19494453X-RAY DIFFRACTION98
1.46-1.480.22492530.17614537X-RAY DIFFRACTION99
1.48-1.50.19382500.16554564X-RAY DIFFRACTION100
1.5-1.520.19452600.15184541X-RAY DIFFRACTION100
1.52-1.540.18152250.13934522X-RAY DIFFRACTION99
1.54-1.560.162190.14034578X-RAY DIFFRACTION100
1.56-1.580.18422480.14224546X-RAY DIFFRACTION99
1.58-1.610.18922310.14134537X-RAY DIFFRACTION99
1.61-1.630.21322280.16114491X-RAY DIFFRACTION99
1.64-1.660.18032400.15784524X-RAY DIFFRACTION99
1.66-1.690.16512840.14844473X-RAY DIFFRACTION99
1.69-1.730.18842340.1494470X-RAY DIFFRACTION98
1.73-1.760.17642280.13594434X-RAY DIFFRACTION96
1.76-1.80.16662740.1214453X-RAY DIFFRACTION98
1.8-1.840.17782180.12314572X-RAY DIFFRACTION100
1.84-1.890.18072500.12954571X-RAY DIFFRACTION100
1.89-1.940.16622700.13634510X-RAY DIFFRACTION99
1.94-20.19092600.15254539X-RAY DIFFRACTION100
2-2.060.20932380.15064567X-RAY DIFFRACTION100
2.06-2.130.18432660.14774557X-RAY DIFFRACTION100
2.13-2.220.18572320.14984571X-RAY DIFFRACTION100
2.22-2.320.16522040.14964587X-RAY DIFFRACTION99
2.32-2.440.17262490.13924425X-RAY DIFFRACTION97
2.44-2.60.17721970.154558X-RAY DIFFRACTION99
2.6-2.80.18482350.15994650X-RAY DIFFRACTION100
2.8-3.080.17562230.16364602X-RAY DIFFRACTION99
3.08-3.520.20393030.17184532X-RAY DIFFRACTION100
3.52-4.440.17931810.15974665X-RAY DIFFRACTION99
4.44-48.660.2012520.18614549X-RAY DIFFRACTION96

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