+Open data
-Basic information
Entry | Database: PDB / ID: 3pkv | ||||||
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Title | Crystal Structure of Toxoflavin Lyase (TflA) | ||||||
Components | Toxoflavin lyase (TflA) | ||||||
Keywords | LYASE / Metalloenzyme / Vicinal oxygen chelate superfamily | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Paenibacillus Polymyxa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.34 Å | ||||||
Authors | Fenwick, M.K. / Philmus, B. / Begley, T.P. / Ealick, S.E. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Toxoflavin lyase requires a novel 1-his-2-carboxylate facial triad . Authors: Fenwick, M.K. / Philmus, B. / Begley, T.P. / Ealick, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pkv.cif.gz | 63.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pkv.ent.gz | 45.3 KB | Display | PDB format |
PDBx/mmJSON format | 3pkv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3pkv_validation.pdf.gz | 413.9 KB | Display | wwPDB validaton report |
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Full document | 3pkv_full_validation.pdf.gz | 415.8 KB | Display | |
Data in XML | 3pkv_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 3pkv_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pk/3pkv ftp://data.pdbj.org/pub/pdb/validation_reports/pk/3pkv | HTTPS FTP |
-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: 28327.756 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paenibacillus Polymyxa (bacteria) / Strain: JH2 / Gene: tflA / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E3SET7*PLUS |
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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: 2.41 Å3/Da / Density % sol: 49.01 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: 1.2M NaH2PO4, 0.8M K2HPO4, 0.1M CAPS (pH 10.5), 0.2M Li2SO4, vapor diffusion, hanging drop, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 26, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Cryo-Cooled Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 4.7 % / Av σ(I) over netI: 29.22 / Number: 136728 / Rmerge(I) obs: 0.07 / Χ2: 1.47 / D res high: 1.7 Å / D res low: 50 Å / Num. obs: 29332 / % possible obs: 99.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.34→50 Å / Num. obs: 59565 / % possible obs: 99.9 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.043 / Χ2: 1.042 / Net I/σ(I): 20.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.34→27.786 Å / Occupancy max: 1 / Occupancy min: 0.25 / SU ML: 0.11 / σ(F): 0.14 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.809 Å2 / ksol: 0.409 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 57.9 Å2 / Biso mean: 17.688 Å2 / Biso min: 7.56 Å2
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Refinement step | Cycle: LAST / Resolution: 1.34→27.786 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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