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Yorodumi- PDB-5g33: Structure of Rad14 in complex with acetylnaphtyl-guanine containi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5g33 | |||||||||
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Title | Structure of Rad14 in complex with acetylnaphtyl-guanine containing DNA | |||||||||
Components |
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Keywords | CELL CYCLE / DNA REPAIR / NUCLEOTIDE EXCISION REPAIR | |||||||||
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 (brewer's yeast) SYNTHETIC CONSTRUCT (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Simon, N. / Ebert, C. / Schneider, S. | |||||||||
Citation | Journal: Chemistry / Year: 2016 Title: Structural Basis for Bulky Adduct DNA Lesion Recognition by the Nucleotide Excision Repair Protein Rad14. Authors: Schneider, S. / Simon, N. / Ebert, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5g33.cif.gz | 170.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g33.ent.gz | 134.1 KB | Display | PDB format |
PDBx/mmJSON format | 5g33.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5g33_validation.pdf.gz | 467.4 KB | Display | wwPDB validaton report |
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Full document | 5g33_full_validation.pdf.gz | 478.4 KB | Display | |
Data in XML | 5g33_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 5g33_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/5g33 ftp://data.pdbj.org/pub/pdb/validation_reports/g3/5g33 | HTTPS FTP |
-Related structure data
Related structure data | 5g32C 5g34C 5g35C 5a3dS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 15612.728 Da / Num. of mol.: 2 / Fragment: RESIDUES 188-306 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Gene: RAD14, YMR201C, YM8325.02C / Production host: ESCHERICHIA COLI BL21 (bacteria) / References: UniProt: P28519 #2: DNA chain | Mass: 4688.142 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SYNTHETIC CONSTRUCT (others) #3: DNA chain | Mass: 4384.865 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SYNTHETIC CONSTRUCT (others) #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | GUANOSINE AT POS.8 IS MODIFIED AT C8 BY ACETYLAMIN | |
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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: 1.9 Å3/Da / Density % sol: 0.43 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.979 |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Sep 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→41.4 Å / Num. obs: 14071 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.39 / Mean I/σ(I) obs: 1.1 / % possible all: 98 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5A3D Resolution: 2.4→53.37 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.894 / SU B: 39.673 / SU ML: 0.413 / Cross valid method: THROUGHOUT / ESU R: 1.053 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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 mean: 56.51 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→53.37 Å
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Refine LS restraints |
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