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Yorodumi- PDB-5lcl: STRUCTURE OF the RAD14 DNA-binding domain IN COMPLEX WITH C8-amin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lcl | ||||||
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Title | STRUCTURE OF the RAD14 DNA-binding domain IN COMPLEX WITH C8-aminofluorene- GUANINE CONTAINING DNA | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / Nucleotide excision repair DNA damage recognition | ||||||
Function / homology | Function and homology information nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair, DNA damage recognition / UV-damage excision repair / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / base-excision repair / damaged DNA binding / DNA damage response / zinc ion binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) Saccharomyces (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Schneider, S. / Carell, T. / Ebert, C. / Simon, N. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Chembiochem / Year: 2017 Title: Structural Insights into the Recognition of N(2) -Aryl- and C8-Aryl DNA Lesions by the Repair Protein XPA/Rad14. Authors: Ebert, C. / Simon, N. / Schneider, S. / Carell, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lcl.cif.gz | 174.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lcl.ent.gz | 135.3 KB | Display | PDB format |
PDBx/mmJSON format | 5lcl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lcl_validation.pdf.gz | 447.2 KB | Display | wwPDB validaton report |
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Full document | 5lcl_full_validation.pdf.gz | 452.9 KB | Display | |
Data in XML | 5lcl_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 5lcl_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/5lcl ftp://data.pdbj.org/pub/pdb/validation_reports/lc/5lcl | HTTPS FTP |
-Related structure data
Related structure data | 5lcmC 5g32S 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 4 / Auth seq-ID: 188 - 299
NCS oper:
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-Components
-DNA repair protein ... , 2 types, 2 molecules AB
#1: Protein | Mass: 14224.176 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RAD14, YMR201C, YM8325.02C / Plasmid: pIBA35 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P28519 |
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#2: Protein | Mass: 43116.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RAD14, YMR201C, YM8325.02C / Plasmid: pIBA35 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P28519 |
-DNA chain , 2 types, 2 molecules CD
#3: DNA chain | Mass: 4668.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces (fungus) |
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#4: DNA chain | Mass: 4674.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces (fungus) |
-Non-polymers , 2 types, 51 molecules
#5: Chemical | #6: 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 grow | Temperature: 277 K / Method: vapor diffusion Details: 0.22M ammonium nitrate 38% 2-methyl-1,3,-propanediol |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→49.3 Å / Num. obs: 18314 / % possible obs: 99 % / Redundancy: 7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.168 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.6 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5G32 Resolution: 2.2→49.3 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.916 / SU B: 17.418 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.378 / ESU R Free: 0.241 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.035 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→49.3 Å
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Refine LS restraints |
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