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- PDB-9f8n: Crystal Structure of PhzA/B from Burkholderia cepacia R18194 in c... -

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Basic information

Entry
Database: PDB / ID: 9f8n
TitleCrystal Structure of PhzA/B from Burkholderia cepacia R18194 in complex with [6-Hydroxy-2-(4-hydroxyphenyl)benzo[b]thiophen-3-yl][2-(isobutylamino)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: 1.32 Å
AuthorsThiemann, M. / Zimmermann, 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)44,0816
Polymers43,0622
Non-polymers1,0194
Water6,846380
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6450 Å2
ΔGint-27 kcal/mol
Surface area13670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.016, 68.849, 54.170
Angle α, β, γ (deg.)90.00, 100.72, 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-A1IAD / [2-(4-hydroxyphenyl)-6-oxidanyl-1-benzothiophen-3-yl]-[2-(2-methylpropylamino)phenyl]methanone / [6-Hydroxy-2-(4-hydroxyphenyl)benzo[b]thiophen-3-yl][2-(isobutylamino)phenyl]methanone


Mass: 417.520 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H23NO3S / Feature type: SUBJECT OF INVESTIGATION
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 16.7% (w/v) PEG 3350, 0.1 M MES pH 6.48, 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: Feb 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.32→42.03 Å / Num. obs: 90832 / % possible obs: 98.5 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.017 / Rrim(I) all: 0.043 / Χ2: 0.89 / Net I/σ(I): 20.5 / Num. measured all: 601099
Reflection shellResolution: 1.32→1.39 Å / % possible obs: 94.7 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.455 / Num. measured all: 73865 / Num. unique obs: 12735 / CC1/2: 0.938 / Rpim(I) all: 0.203 / Rrim(I) all: 0.5 / Χ2: 0.67 / Net I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSJan 10, 2022data reduction
Aimlessv0.7.7data scaling
PHASERv2.8.3phasing
autoPROCv1.0.5 (20211020)data processing
PDB_EXTRACTv4.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.32→42.03 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 15.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1604 4440 4.89 %
Rwork0.1354 --
obs0.1366 90741 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.218 Å2
Refinement stepCycle: LAST / Resolution: 1.32→42.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2480 0 72 380 2932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012834
X-RAY DIFFRACTIONf_angle_d1.0723861
X-RAY DIFFRACTIONf_dihedral_angle_d15.9721019
X-RAY DIFFRACTIONf_chiral_restr0.084359
X-RAY DIFFRACTIONf_plane_restr0.011516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.32-1.330.26161330.25722547X-RAY DIFFRACTION88
1.33-1.350.27041490.23012713X-RAY DIFFRACTION92
1.35-1.360.23841560.19822785X-RAY DIFFRACTION97
1.36-1.380.20871780.1822863X-RAY DIFFRACTION99
1.38-1.40.18321450.16932855X-RAY DIFFRACTION99
1.4-1.420.16391280.15232906X-RAY DIFFRACTION99
1.42-1.440.19921360.14412926X-RAY DIFFRACTION99
1.44-1.460.18931510.13612902X-RAY DIFFRACTION99
1.46-1.480.21531550.13092859X-RAY DIFFRACTION99
1.48-1.510.18341870.12212916X-RAY DIFFRACTION100
1.51-1.530.14331180.11462878X-RAY DIFFRACTION99
1.53-1.560.14241660.11382888X-RAY DIFFRACTION99
1.56-1.590.15841410.11962913X-RAY DIFFRACTION99
1.59-1.620.1451450.1112841X-RAY DIFFRACTION98
1.62-1.660.13981260.11832869X-RAY DIFFRACTION98
1.66-1.70.17571450.12042902X-RAY DIFFRACTION99
1.7-1.740.16051570.12172914X-RAY DIFFRACTION99
1.74-1.790.15081360.11852903X-RAY DIFFRACTION99
1.79-1.840.13711410.11442914X-RAY DIFFRACTION99
1.84-1.90.15631320.11332927X-RAY DIFFRACTION99
1.9-1.970.13911640.11772884X-RAY DIFFRACTION100
1.97-2.040.1481680.1192899X-RAY DIFFRACTION99
2.04-2.140.14591370.12172938X-RAY DIFFRACTION99
2.14-2.250.16251330.12372872X-RAY DIFFRACTION97
2.25-2.390.15941790.11862856X-RAY DIFFRACTION99
2.39-2.580.14271280.1232985X-RAY DIFFRACTION100
2.58-2.830.1421620.1372887X-RAY DIFFRACTION99
2.83-3.240.17391390.14252923X-RAY DIFFRACTION99
3.25-4.090.14861550.13542919X-RAY DIFFRACTION99
4.09-42.030.18011500.1642917X-RAY DIFFRACTION97

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