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Yorodumi- PDB-3ex9: Crystal structure of PhzA/B from Burkholderia cepacia R18194 crys... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ex9 | ||||||
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Title | Crystal structure of PhzA/B from Burkholderia cepacia R18194 crystallized in C2221 | ||||||
Components | Phenazine biosynthesis protein A/B | ||||||
Keywords | BIOSYNTHETIC PROTEIN / phenazine biosynthesis / KSI | ||||||
Function / homology | Phenazine biosynthesis protein A/B / Phenazine biosynthesis protein A/B / Nuclear Transport Factor 2; Chain: A, - #50 / antibiotic biosynthetic process / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Phenazine biosynthesis protein A/B Function and homology information | ||||||
Biological species | Burkholderia sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Ahuja, E.G. / 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 | 3ex9.cif.gz | 46.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ex9.ent.gz | 31.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ex9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/3ex9 ftp://data.pdbj.org/pub/pdb/validation_reports/ex/3ex9 | HTTPS FTP |
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-Related structure data
Related structure data | 3b4oSC 3b4pC 3cnmC 3dzlC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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.: 1 / Fragment: PhzA/B Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia sp. (bacteria) / Strain: R18194 / Gene: Bcep18194_B1568 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 pLysS / References: UniProt: Q396C9 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.57 % |
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Crystal grow | Temperature: 284 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 0.1M Bis-TRIS, 0.2M NH4OAc, 20% (w/v) PEG 3350, pH 6.2, 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: 2.2→42.26 Å / Num. all: 10609 / Num. obs: 10338 / % possible obs: 97.4 % / Observed criterion σ(I): 5.5 / Redundancy: 9.2 % / Biso Wilson estimate: 48 Å2 / Rsym value: 0.064 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 2.1→2.3 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 5.5 / Num. unique all: 1305 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3B4O Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.916 / SU B: 16.581 / SU ML: 0.179 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; TLS-REFINEMENT WAS USED THROUGOUT (1 BODY)
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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: 54.538 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -11.0642 Å / Origin y: 1.1891 Å / Origin z: -14.952 Å
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