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Yorodumi- PDB-3jun: Crystal Structure of PhzA/B from Burkholderia cepacia R18194 in s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jun | ||||||
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Title | Crystal Structure of PhzA/B from Burkholderia cepacia R18194 in simultaneous complex with racemic 5-bromo-2-(piperidin-3-ylamino)benzoic acid | ||||||
Components | Phenazine biosynthesis protein A/B | ||||||
Keywords | BIOSYNTHETIC PROTEIN / chirality / drug design / phenazine biosynthesis / racemate / racemic mixture | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Burkholderia sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å | ||||||
Authors | Mentel, M. / Breinbauer, R. / Blankenfeldt, W. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2009 Title: The Active Site of an Enzyme Can Host Both Enantiomers of a Racemic Ligand Simultaneously Authors: Mentel, M. / Blankenfeldt, W. / Breinbauer, R. #1: Journal: J.Am.Chem.Soc. / Year: 2008 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3jun.cif.gz | 83 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jun.ent.gz | 62.7 KB | Display | PDB format |
PDBx/mmJSON format | 3jun.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ju/3jun ftp://data.pdbj.org/pub/pdb/validation_reports/ju/3jun | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | biological unit is the same as asym. |
-Components
#1: Protein | Mass: 21531.025 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia sp. (bacteria) / Strain: 383 / Gene: Bcep18194_B1568 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) pLysS / References: UniProt: Q396C9 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.59 % |
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Crystal grow | Temperature: 284 K Details: 16-20% (w/v) PEG3350, 0.2 M NH4OAc, 0.1 M Bis-Tris pH 6.1-6.7; complex prepared by overnight soaking in mother liquor containing 4 mM racemic 5-bromo-2-(piperidin-3-ylamino)benzoic acid, ...Details: 16-20% (w/v) PEG3350, 0.2 M NH4OAc, 0.1 M Bis-Tris pH 6.1-6.7; complex prepared by overnight soaking in mother liquor containing 4 mM racemic 5-bromo-2-(piperidin-3-ylamino)benzoic acid, vapor diffusion, hanging drop, temperature 284K PH range: 6.1 - 6.7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98407 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 27, 2007 / Details: SI(111) |
Radiation | Monochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98407 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→19.7 Å / Num. obs: 37044 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 37.23 Å2 |
Reflection shell | Resolution: 1.8→1.9 Å / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 4.2 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Resolution: 1.8→19.7 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.105 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.73 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→19.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.85 Å
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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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