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Yorodumi- PDB-3edn: Crystal structure of the Bacillus anthracis phenazine biosynthesi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3edn | ||||||
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Title | Crystal structure of the Bacillus anthracis phenazine biosynthesis protein, PhzF family | ||||||
Components | Phenazine biosynthesis protein, PhzF family | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Diaminopimelate epimerase-like fold / Alpha and beta protein class / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Anderson, S.M. / Brunzelle, J.S. / Onopriyenko, O. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the Bacillus anthracis phenazine biosynthesis protein, PhzF family Authors: Anderson, S.M. / Brunzelle, J.S. / Onopriyenko, O. / Savchenko, A. / Anderson, W.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3edn.cif.gz | 151.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3edn.ent.gz | 125 KB | Display | PDB format |
PDBx/mmJSON format | 3edn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3edn_validation.pdf.gz | 449.3 KB | Display | wwPDB validaton report |
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Full document | 3edn_full_validation.pdf.gz | 456.9 KB | Display | |
Data in XML | 3edn_validation.xml.gz | 33.5 KB | Display | |
Data in CIF | 3edn_validation.cif.gz | 52.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/3edn ftp://data.pdbj.org/pub/pdb/validation_reports/ed/3edn | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33739.531 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BAS3216, BA_3469, GBAA3469 / Production host: Escherichia coli (E. coli) / References: UniProt: Q81MV2, UniProt: A0A6L8PH16*PLUS #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-SIN / | #4: Chemical | ChemComp-MG / | #5: 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: 2.19 Å3/Da / Density % sol: 43.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 Details: 2M NH4SO4, 5% isopropanol, pH 7.0, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.5→38.18 Å / Num. all: 95606 / Num. obs: 93368 / % possible obs: 97.8 % / Observed criterion σ(F): 1.6 / Observed criterion σ(I): 2.4 / Redundancy: 5 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 13 | ||||||||||||||||||
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 2.4 / Num. unique all: 8426 / % possible all: 89.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→38.18 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 1.451 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 56.72 Å2 / Biso mean: 18.204 Å2 / Biso min: 7.2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→38.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.501→1.54 Å / Total num. of bins used: 20
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