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- PDB-3juq: Crystal Structure of PhzA/B from Burkholderia cepacia R18194 cocr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3juq | ||||||
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Title | Crystal Structure of PhzA/B from Burkholderia cepacia R18194 cocrystallized with 2 mM racemic 5-bromo-2-(piperidin-3-ylamino)benzoic acid | ||||||
![]() | Phenazine biosynthesis protein A/B | ||||||
![]() | BIOSYNTHETIC PROTEIN / chirality / drug design / phenazine biosynthesis / racemate / racemic mixture | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Mentel, M. / Breinbauer, R. / Blankenfeldt, W. | ||||||
![]() | ![]() Title: The Active Site of an Enzyme Can Host Both Enantiomers of a Racemic Ligand Simultaneously Authors: Mentel, M. / Blankenfeldt, W. / Breinbauer, R. #1: ![]() Title: PhzA/B catalyzes the formation of the tricycle in phenazine biosynthesis Authors: Ahuja, E.G. / Janning, P. / Graebsch, A. / Breinbauer, R. / Hiller, W. / Costisella, B. / Thomashow, L.S. / Mavrodi, D.V. / Blankenfeldt, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.4 KB | Display | ![]() |
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PDB format | ![]() | 67.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21531.025 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.88 % |
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Crystal grow | Temperature: 284 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 28% (w/v) PEG3350, 0.2 M NH4OAc, 0.1 M Bis-Tris pH 6.1-6.7; complex prepared by cocrystallization with 2 mM racemic 5-bromo-2-(piperidin-3-ylamino)benzoic acid, vapor diffusion, hanging drop, temperature 284K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 27, 2007 / Details: SI(111) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98407 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→19.61 Å / Num. obs: 75067 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 39.344 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 21.37 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Rmerge(I) obs: 0.03 / Diffraction-ID: 1
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Processing
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Refinement | Resolution: 1.75→19.61 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.188 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.657 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→19.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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