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Yorodumi- PDB-3dzl: Crystal structure of PhzA/B from Burkholderia cepacia R18194 in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dzl | ||||||
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Title | Crystal structure of PhzA/B from Burkholderia cepacia R18194 in complex with (R)-3-oxocyclohexanecarboxylic acid | ||||||
Components | Phenazine biosynthesis protein A/B | ||||||
Keywords | BIOSYNTHETIC PROTEIN / phenazine biosynthesis | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Burkholderia sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å | ||||||
Authors | Ahuja, E.G. / Mentel, M. / Graebsch, A. / Breinbauer, R. / Blankenfeldt, W. | ||||||
Citation | 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. / Mentel, M. / 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 | 3dzl.cif.gz | 88.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dzl.ent.gz | 68.1 KB | Display | PDB format |
PDBx/mmJSON format | 3dzl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/3dzl ftp://data.pdbj.org/pub/pdb/validation_reports/dz/3dzl | 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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-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) / Gene: Bcep18194_B1568 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 pLysS / References: UniProt: Q396C9 #2: Chemical | ChemComp-3OC / ( #3: 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: 45.63 % |
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Crystal grow | Temperature: 284 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 16-20% (w/v) PEG 3350, 0.2 M NH4OAc, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 284K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 20, 2008 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→20 Å / Num. all: 40329 / Num. obs: 40290 / % possible obs: 99.9 % / Observed criterion σ(I): 4.9 / Redundancy: 8.5 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 24.1 |
Reflection shell | Resolution: 1.75→1.85 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 4.9 / Num. unique all: 6075 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.75→19.39 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.278 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, TLS-REFINEMENT (1 BODY) WAS USED THROUGHOUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.08 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→19.39 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 / Origin x: 36.6423 Å / Origin y: 6.131 Å / Origin z: 79.6803 Å
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