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Yorodumi- PDB-4fhd: Spore photoproduct lyase complexed with dinucleoside spore photop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fhd | ||||||
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Title | Spore photoproduct lyase complexed with dinucleoside spore photoproduct | ||||||
Components | Spore photoproduct lyase | ||||||
Keywords | LYASE / partial TIM-barrel / DNA repair / damaged DNA | ||||||
Function / homology | Function and homology information DNA photolyase activity / endospore-forming forespore / S-adenosyl-L-methionine binding / 4 iron, 4 sulfur cluster binding / metal ion binding Similarity search - Function | ||||||
Biological species | Geobacillus thermodenitrificans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Benjdia, A. / Heil, K. / Barends, T.R.M. / Carell, T. / Schlichting, I. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2012 Title: Structural insights into recognition and repair of UV-DNA damage by Spore Photoproduct Lyase, a radical SAM enzyme. Authors: Benjdia, A. / Heil, K. / Barends, T.R. / Carell, T. / Schlichting, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fhd.cif.gz | 91 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fhd.ent.gz | 66.3 KB | Display | PDB format |
PDBx/mmJSON format | 4fhd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/4fhd ftp://data.pdbj.org/pub/pdb/validation_reports/fh/4fhd | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 42975.910 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus thermodenitrificans (bacteria) Strain: NG80-2 / Gene: GTNG_2348 / Plasmid: modified pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE-3) / References: UniProt: A4IQU1 |
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-Non-polymers , 6 types, 121 molecules
#2: Chemical | ChemComp-SF4 / | ||||||
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#3: Chemical | ChemComp-EEM / [( | ||||||
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-0TT / | #6: Chemical | ChemComp-POP / | #7: 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: 48.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 200 mM Li-sulfate, 100 mM Tris/HCl, 19-27% PEG800, 70 mM HEGA-8, anaerobically , pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2011 |
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→71.93 Å / Num. all: 28692 / Num. obs: 28692 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.071 |
Reflection shell | Resolution: 2→2.1 Å / Rmerge(I) obs: 0.484 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: wt structure without substrate Resolution: 2→71.93 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.899 / SU B: 3.594 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 2.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 3.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.514 Å2
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Refinement step | Cycle: LAST / Resolution: 2→71.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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