+Open data
-Basic information
Entry | Database: PDB / ID: 4k9r | ||||||
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Title | Spore photoproduct lyase Y98F mutant | ||||||
Components | Spore photoproduct lyase | ||||||
Keywords | LYASE / partial TIM barrel / DNA repair | ||||||
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: 2.3 Å | ||||||
Authors | Yang, L. / Nelson, R.S. / Benjdia, A. / Lin, G. / Telser, J. / Stoll, S. / Schlichting, I. / Li, L. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: A radical transfer pathway in spore photoproduct lyase. Authors: Yang, L. / Nelson, R.S. / Benjdia, A. / Lin, G. / Telser, J. / Stoll, S. / Schlichting, I. / Li, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k9r.cif.gz | 88.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k9r.ent.gz | 65.3 KB | Display | PDB format |
PDBx/mmJSON format | 4k9r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/4k9r ftp://data.pdbj.org/pub/pdb/validation_reports/k9/4k9r | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 42959.910 Da / Num. of mol.: 1 / Mutation: Y98F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus thermodenitrificans (bacteria) Strain: NG80-2 / Gene: GTNG_2348 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) / References: UniProt: A4IQU1, EC: 4.1.99.14 | ||
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#2: Chemical | ChemComp-SF4 / | ||
#3: Chemical | ChemComp-EEM / [( | ||
#4: Chemical | ChemComp-SO4 / #5: 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: 2.81 Å3/Da / Density % sol: 56.26 % |
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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% PEG8000, 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: 0.9786 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 26, 2011 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→43.06 Å / Num. all: 22170 / Num. obs: 22170 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Rmerge(I) obs: 0.132 |
Reflection shell | Resolution: 2.3→2.4 Å / Rmerge(I) obs: 0.674 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→43.06 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.913 / SU B: 6.832 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.233
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.191 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→43.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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