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- PDB-9f8p: Crystal Structure of PhzA/B from Burkholderia cepacia R18194 in c... -

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Basic information

Entry
Database: PDB / ID: 9f8p
TitleCrystal Structure of PhzA/B from Burkholderia cepacia R18194 in complex with [6-Hydroxy-2-(4-hydroxyphenyl)benzo[b]thiophen-3-yl](4-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: 1.36 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)44,2288
Polymers43,0622
Non-polymers1,1666
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-9 kcal/mol
Surface area14110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.059, 69.104, 54.144
Angle α, β, γ (deg.)90.00, 100.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q396C9

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Non-polymers , 5 types, 259 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#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-A1IAI / (4-hydroxyphenyl)-[2-(4-hydroxyphenyl)-6-oxidanyl-1-benzothiophen-3-yl]methanone / [6-Hydroxy-2-(4-hydroxyphenyl)benzo[b]thiophen-3- yl](4-hydroxyphenyl)methanone


Mass: 362.398 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H14O4S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 293 K / Method: vapor diffusion, sitting drop
Details: 18.3% (w/v) PEG 3350, 0.1 M MES pH 6.37, 0.278 M ammonium acetate, 6.67% (v/v) 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: Apr 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.36→53.12 Å / Num. obs: 82562 / % possible obs: 98.9 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.024 / Rrim(I) all: 0.064 / Net I/σ(I): 14.1
Reflection shellResolution: 1.36→1.39 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.706 / Mean I/σ(I) obs: 2 / Num. unique obs: 4182 / CC1/2: 0.882 / Rpim(I) all: 0.288 / Rrim(I) all: 0.763

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Processing

Software
NameVersionClassification
XDSJan 10, 2022data 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: 1.36→53.12 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 16.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1641 4048 4.91 %
Rwork0.1362 --
obs0.1376 82521 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.575 Å2
Refinement stepCycle: LAST / Resolution: 1.36→53.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2526 0 80 253 2859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012741
X-RAY DIFFRACTIONf_angle_d1.1823721
X-RAY DIFFRACTIONf_dihedral_angle_d16.0811043
X-RAY DIFFRACTIONf_chiral_restr0.086352
X-RAY DIFFRACTIONf_plane_restr0.014515
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.380.25961760.24562716X-RAY DIFFRACTION100
1.38-1.40.2812940.2172750X-RAY DIFFRACTION100
1.4-1.410.24451410.19582736X-RAY DIFFRACTION100
1.41-1.430.22431400.17462680X-RAY DIFFRACTION100
1.43-1.450.23181370.15742660X-RAY DIFFRACTION99
1.45-1.470.19321400.14912744X-RAY DIFFRACTION99
1.47-1.490.19451330.14232702X-RAY DIFFRACTION99
1.49-1.520.17261230.13042658X-RAY DIFFRACTION98
1.52-1.540.13641300.12562697X-RAY DIFFRACTION97
1.54-1.570.17711330.13312535X-RAY DIFFRACTION93
1.57-1.60.17541640.12662673X-RAY DIFFRACTION99
1.6-1.630.16391330.122696X-RAY DIFFRACTION100
1.63-1.660.14421260.12022736X-RAY DIFFRACTION100
1.66-1.70.15261680.12022677X-RAY DIFFRACTION99
1.7-1.740.1841600.1232709X-RAY DIFFRACTION100
1.74-1.780.17011110.1232726X-RAY DIFFRACTION100
1.78-1.830.15331170.1192785X-RAY DIFFRACTION100
1.83-1.880.17981240.11712714X-RAY DIFFRACTION100
1.88-1.940.13741520.11322721X-RAY DIFFRACTION99
1.94-2.010.12561390.1162693X-RAY DIFFRACTION99
2.01-2.090.14011290.12422713X-RAY DIFFRACTION98
2.09-2.190.16531370.12832585X-RAY DIFFRACTION95
2.19-2.30.14751370.12332758X-RAY DIFFRACTION100
2.3-2.450.15681400.1172740X-RAY DIFFRACTION100
2.45-2.640.14091620.1282696X-RAY DIFFRACTION100
2.64-2.90.15991630.13532721X-RAY DIFFRACTION100
2.9-3.320.18871710.14152714X-RAY DIFFRACTION99
3.32-4.190.15131240.13322731X-RAY DIFFRACTION98
4.19-53.120.17851440.16652807X-RAY DIFFRACTION100

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