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- PDB-9f8r: Crystal Structure of PhzA/B from Burkholderia cepacia R18194 in c... -

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Basic information

Entry
Database: PDB / ID: 9f8r
TitleCrystal Structure of PhzA/B from Burkholderia cepacia R18194 in complex with (4-Chlorophenyl)[2-(4-hydroxyphenyl)benzo[b]thiophen-3-yl]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 / : / ACETATE ION / Phenazine biosynthesis protein A/B
Function and homology information
Biological speciesBurkholderia lata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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)88,61016
Polymers86,1244
Non-polymers2,48612
Water8,809489
1
A: Phenazine biosynthesis protein A/B
B: Phenazine biosynthesis protein A/B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2447
Polymers43,0622
Non-polymers1,1825
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint3 kcal/mol
Surface area13820 Å2
MethodPISA
2
C: Phenazine biosynthesis protein A/B
D: Phenazine biosynthesis protein A/B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3659
Polymers43,0622
Non-polymers1,3037
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint7 kcal/mol
Surface area13740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.933, 69.015, 83.350
Angle α, β, γ (deg.)90.00, 90.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

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

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Non-polymers , 5 types, 501 molecules

#2: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-A1IAN / (4-chlorophenyl)-[2-(4-hydroxyphenyl)-1-benzothiophen-3-yl]methanone / (4-Chlorophenyl)[2-(4-hydroxyphenyl)benzo[b]thiophen3-yl]methanone


Mass: 364.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H13ClO2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / 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: 2.42 Å3/Da / Density % sol: 49.8 %
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: 1.0331 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0331 Å / Relative weight: 1
ReflectionResolution: 1.58→69.93 Å / Num. obs: 107445 / % possible obs: 98.9 % / Redundancy: 7 % / CC1/2: 0.985 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.053 / Rrim(I) all: 0.142 / Net I/σ(I): 8
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.271 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 5343 / CC1/2: 0.875 / Rpim(I) all: 0.505 / Rrim(I) all: 1.37 / % possible all: 98.8

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Processing

Software
NameVersionClassification
XDSJun 30, 2023data reduction
Aimlessv0.7.9data 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: 1.58→53.63 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2168 5145 4.81 %
Rwork0.1926 --
obs0.1938 107022 98.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.979 Å2
Refinement stepCycle: LAST / Resolution: 1.58→53.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4961 0 164 489 5614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015424
X-RAY DIFFRACTIONf_angle_d1.117369
X-RAY DIFFRACTIONf_dihedral_angle_d15.572051
X-RAY DIFFRACTIONf_chiral_restr0.067703
X-RAY DIFFRACTIONf_plane_restr0.0131010
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.60.3551530.32423400X-RAY DIFFRACTION98
1.6-1.620.37911930.29063335X-RAY DIFFRACTION99
1.62-1.640.28021900.27773395X-RAY DIFFRACTION99
1.64-1.660.30471940.26883342X-RAY DIFFRACTION98
1.66-1.680.31481600.25483383X-RAY DIFFRACTION99
1.68-1.70.23371720.23483386X-RAY DIFFRACTION99
1.7-1.730.23241940.21713342X-RAY DIFFRACTION98
1.73-1.750.2371660.20453450X-RAY DIFFRACTION99
1.75-1.780.25481450.20323370X-RAY DIFFRACTION98
1.78-1.810.25092000.20023404X-RAY DIFFRACTION99
1.81-1.840.21471750.19953394X-RAY DIFFRACTION99
1.84-1.870.23351860.19463368X-RAY DIFFRACTION99
1.87-1.910.22551500.20213434X-RAY DIFFRACTION99
1.91-1.950.28431680.21043412X-RAY DIFFRACTION99
1.95-1.990.2231390.21073426X-RAY DIFFRACTION99
1.99-2.040.21311880.18563398X-RAY DIFFRACTION99
2.04-2.090.23811250.18623354X-RAY DIFFRACTION96
2.09-2.140.22671420.18723236X-RAY DIFFRACTION94
2.14-2.210.23381360.19293429X-RAY DIFFRACTION99
2.21-2.280.23851520.19373416X-RAY DIFFRACTION99
2.28-2.360.20921290.1893472X-RAY DIFFRACTION99
2.36-2.460.25122120.18293389X-RAY DIFFRACTION99
2.46-2.570.211680.18943432X-RAY DIFFRACTION100
2.57-2.70.2091790.19563431X-RAY DIFFRACTION100
2.7-2.870.19482300.18873391X-RAY DIFFRACTION99
2.87-3.090.1931730.1813427X-RAY DIFFRACTION99
3.09-3.40.21851720.18333453X-RAY DIFFRACTION99
3.4-3.90.16841950.16633298X-RAY DIFFRACTION95
3.9-4.910.16341700.1483415X-RAY DIFFRACTION98
4.91-53.630.22531890.21753495X-RAY DIFFRACTION99

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