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- PDB-9f8l: Crystal Structure of PhzA/B from Burkholderia cepacia R18194 in c... -

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Basic information

Entry
Database: PDB / ID: 9f8l
TitleCrystal Structure of PhzA/B from Burkholderia cepacia R18194 in complex with [6-Hydroxy-2-(4-hydroxyphenyl)benzo[b]thiophen-3-yl](3-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: 1.38 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)44,54610
Polymers43,0622
Non-polymers1,4848
Water6,233346
1
A: Phenazine biosynthesis protein A/B
hetero molecules

A: Phenazine biosynthesis protein A/B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3628
Polymers43,0622
Non-polymers1,2996
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area5770 Å2
ΔGint-9 kcal/mol
Surface area14560 Å2
MethodPISA
2
B: Phenazine biosynthesis protein A/B
hetero molecules

B: Phenazine biosynthesis protein A/B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,73012
Polymers43,0622
Non-polymers1,66810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6210 Å2
ΔGint-7 kcal/mol
Surface area14200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.995, 69.369, 69.182
Angle α, β, γ (deg.)90.00, 93.64, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-205-

GOL

21A-441-

HOH

31B-440-

HOH

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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-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-A1IAL / (3-hydroxyphenyl)-[2-(4-hydroxyphenyl)-6-oxidanyl-1-benzothiophen-3-yl]methanone / [6-Hydroxy-2-(4-hydroxyphenyl)benzo[b]thiophen-3-yl](3-hydroxyphenyl)methanone


Mass: 362.398 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H14O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.37 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 15% (w/v) PEG monomethyl ether, 0.1 M MES pH 6.14, 0.122 M ammonium acetate, 5% (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: May 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.38→53.18 Å / Num. obs: 79713 / % possible obs: 99.1 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.019 / Rrim(I) all: 0.051 / Net I/σ(I): 16.5
Reflection shellResolution: 1.38→1.4 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.686 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3936 / CC1/2: 0.897 / Rpim(I) all: 0.278 / Rrim(I) all: 0.741

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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: 1.38→42.99 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1641 3961 4.97 %
Rwork0.1373 --
obs0.1386 79659 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.879 Å2
Refinement stepCycle: LAST / Resolution: 1.38→42.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2548 0 100 346 2994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012904
X-RAY DIFFRACTIONf_angle_d1.1723953
X-RAY DIFFRACTIONf_dihedral_angle_d17.6231071
X-RAY DIFFRACTIONf_chiral_restr0.085371
X-RAY DIFFRACTIONf_plane_restr0.011526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.40.29211220.22562657X-RAY DIFFRACTION99
1.4-1.410.2361300.20092722X-RAY DIFFRACTION99
1.41-1.430.2191570.17662682X-RAY DIFFRACTION99
1.43-1.450.22631360.16032697X-RAY DIFFRACTION99
1.45-1.470.20321520.15892712X-RAY DIFFRACTION99
1.47-1.490.21041410.15582670X-RAY DIFFRACTION99
1.49-1.520.19651560.1472661X-RAY DIFFRACTION99
1.52-1.540.19871720.14752687X-RAY DIFFRACTION99
1.54-1.570.21051310.16132693X-RAY DIFFRACTION99
1.57-1.60.1671350.1552710X-RAY DIFFRACTION99
1.6-1.630.17141270.14192647X-RAY DIFFRACTION98
1.63-1.660.15811490.12762688X-RAY DIFFRACTION99
1.66-1.70.16391360.12322723X-RAY DIFFRACTION99
1.7-1.740.15421420.11372697X-RAY DIFFRACTION99
1.74-1.780.14681540.11162695X-RAY DIFFRACTION99
1.78-1.830.15251290.11142699X-RAY DIFFRACTION99
1.83-1.880.181310.12362724X-RAY DIFFRACTION99
1.88-1.940.1511370.12832696X-RAY DIFFRACTION99
1.94-2.010.14421490.12472716X-RAY DIFFRACTION99
2.01-2.090.16011340.12332742X-RAY DIFFRACTION99
2.09-2.190.15931340.12692703X-RAY DIFFRACTION99
2.19-2.30.16041190.12642688X-RAY DIFFRACTION98
2.3-2.450.1611450.12532747X-RAY DIFFRACTION100
2.45-2.640.18031350.1322708X-RAY DIFFRACTION100
2.64-2.90.15451730.13382708X-RAY DIFFRACTION99
2.9-3.320.1671620.14082723X-RAY DIFFRACTION99
3.32-4.190.14341330.12742708X-RAY DIFFRACTION98
4.19-42.990.16541400.16392795X-RAY DIFFRACTION99

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