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- PDB-9f8h: Crystal Structure of PhzA/B from Burkholderia cepacia R18194 in c... -

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Basic information

Entry
Database: PDB / ID: 9f8h
TitleCrystal Structure of PhzA/B from Burkholderia cepacia R18194 in complex with Raloxifene
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 / RALOXIFENE / Phenazine biosynthesis protein A/B
Function and homology information
Biological speciesBurkholderia lata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsDiederich, C. / Zimmermann, 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)44,2557
Polymers43,0622
Non-polymers1,1935
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint-20 kcal/mol
Surface area13470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.039, 69.099, 54.217
Angle α, β, γ (deg.)90.00, 101.08, 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-RAL / RALOXIFENE


Mass: 473.583 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H27NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#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.: 264 / 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: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop
Details: 17% (w/v) PEG 3350, 0.1 M Bis-TRIS pH 6.6, 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.47→53.21 Å / Num. obs: 66463 / % possible obs: 99.5 % / Redundancy: 4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.036 / Rrim(I) all: 0.075 / Net I/σ(I): 11.1
Reflection shellResolution: 1.47→1.49 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.955 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3287 / CC1/2: 0.662 / Rpim(I) all: 0.532 / Rrim(I) all: 1.098 / % possible all: 99.6

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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: 1.47→53.21 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 14.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1639 3237 4.88 %
Rwork0.134 --
obs0.1354 66389 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.87 Å2
Refinement stepCycle: LAST / Resolution: 1.47→53.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2490 0 84 264 2838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162744
X-RAY DIFFRACTIONf_angle_d1.3233721
X-RAY DIFFRACTIONf_dihedral_angle_d14.4691077
X-RAY DIFFRACTIONf_chiral_restr0.103347
X-RAY DIFFRACTIONf_plane_restr0.015528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.490.25581230.20042685X-RAY DIFFRACTION98
1.49-1.510.20351400.16992730X-RAY DIFFRACTION99
1.51-1.540.18231810.15122693X-RAY DIFFRACTION99
1.54-1.560.18711290.14962728X-RAY DIFFRACTION99
1.56-1.590.19331470.15152743X-RAY DIFFRACTION99
1.59-1.620.20171360.14432722X-RAY DIFFRACTION99
1.62-1.660.19231070.14672771X-RAY DIFFRACTION100
1.66-1.690.17851550.14742758X-RAY DIFFRACTION100
1.69-1.730.15371210.1332734X-RAY DIFFRACTION100
1.73-1.780.15971650.11932716X-RAY DIFFRACTION100
1.78-1.820.14531420.11242750X-RAY DIFFRACTION100
1.82-1.880.15341540.10582723X-RAY DIFFRACTION99
1.88-1.940.14381640.10882711X-RAY DIFFRACTION99
1.94-2.010.15191590.11932734X-RAY DIFFRACTION100
2.01-2.090.16751480.12422778X-RAY DIFFRACTION100
2.09-2.180.13491330.11372733X-RAY DIFFRACTION100
2.18-2.30.16851250.11362753X-RAY DIFFRACTION100
2.3-2.440.14361350.11492764X-RAY DIFFRACTION99
2.44-2.630.15231330.12562746X-RAY DIFFRACTION100
2.63-2.890.16741440.13682760X-RAY DIFFRACTION100
2.89-3.310.16681400.13842765X-RAY DIFFRACTION100
3.31-4.170.14511310.1332819X-RAY DIFFRACTION99
4.17-53.210.191250.16462836X-RAY DIFFRACTION99

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