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Yorodumi- PDB-3cnm: Crystal Structure of Phenazine Biosynthesis Protein PhzA/B from B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cnm | ||||||
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Title | Crystal Structure of Phenazine Biosynthesis Protein PhzA/B from Burkholderia cepacia R18194, DHHA complex | ||||||
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 / rigid body refinement of apo structure / Resolution: 1.65 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 | 3cnm.cif.gz | 92.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cnm.ent.gz | 69.6 KB | Display | PDB format |
PDBx/mmJSON format | 3cnm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cnm_validation.pdf.gz | 469.7 KB | Display | wwPDB validaton report |
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Full document | 3cnm_full_validation.pdf.gz | 477.5 KB | Display | |
Data in XML | 3cnm_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 3cnm_validation.cif.gz | 29.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/3cnm ftp://data.pdbj.org/pub/pdb/validation_reports/cn/3cnm | HTTPS FTP |
-Related structure data
Related structure data | 3b4oSC 3b4pC 3dzlC 3ex9C 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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Details | dimer |
-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): Rosetta 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: 2.29 Å3/Da / Density % sol: 46.38 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.1 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 50 mM DHHA, VAPOR DIFFUSION, HANGING DROP, temperature 285K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9809 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 6, 2008 / Details: SI(111) monochromator |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9809 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→20 Å / Num. all: 48683 / Num. obs: 48675 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 14.1 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.139 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.65→1.75 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.7 / Num. unique all: 7754 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: rigid body refinement of apo structure Starting model: 3B4O Resolution: 1.65→19.81 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.23 / SU ML: 0.051 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; TLS-Refinement was used throughout (1 TLS 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: 24.467 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→19.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 37.0061 Å / Origin y: 5.9718 Å / Origin z: 79.8364 Å
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Refinement TLS group |
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