[English] 日本語
Yorodumi- PDB-3b4p: Crystal structure of phenazine biosynthesis protein PhzA/B from B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b4p | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of phenazine biosynthesis protein PhzA/B from Burkholderia cepacia R18194, complex with 2-(cyclohexylamino)benzoic acid | ||||||
Components | Phenazine biosynthesis protein A/B | ||||||
Keywords | BIOSYNTHETIC PROTEIN / phenazine biosynthesis / imine / Schiff base | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Burkholderia sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Ahuja, E.G. / Janning, P. / 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3b4p.cif.gz | 85.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3b4p.ent.gz | 65.2 KB | Display | PDB format |
PDBx/mmJSON format | 3b4p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/3b4p ftp://data.pdbj.org/pub/pdb/validation_reports/b4/3b4p | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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: R18194 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 pLysS / References: UniProt: Q396C9 #2: Chemical | #3: Chemical | ChemComp-AZI / | #4: Chemical | ChemComp-ACT / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.09 % |
---|---|
Crystal grow | Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 16-20% (w/v) PEG 3350, 0.2 M NH4-acetate, 0.1 M Bis-TRIS pH 6.1-6.7, soak with 10 mM 2-(cyclohexylamino)benzoic acid in ML, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 285K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9789 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 30, 2007 / Details: Si(111)monochromator |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→19.65 Å / Num. all: 43508 / Num. obs: 43465 / % possible obs: 99.9 % / Observed criterion σ(I): 4 / Redundancy: 14.1 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 24.2 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 4.2 / Num. unique all: 6744 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.7→19.65 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.842 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 28.096 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→19.65 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
|