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Yorodumi- PDB-5g34: Structure of Rad14 in complex with acetylaminoanthracene-C8-guani... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5g34 | ||||||
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Title | Structure of Rad14 in complex with acetylaminoanthracene-C8-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 / 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: 1.9 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 | 5g34.cif.gz | 171.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g34.ent.gz | 134.6 KB | Display | PDB format |
PDBx/mmJSON format | 5g34.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5g34_validation.pdf.gz | 460.3 KB | Display | wwPDB validaton report |
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Full document | 5g34_full_validation.pdf.gz | 473 KB | Display | |
Data in XML | 5g34_validation.xml.gz | 15 KB | Display | |
Data in CIF | 5g34_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/5g34 ftp://data.pdbj.org/pub/pdb/validation_reports/g3/5g34 | HTTPS FTP |
-Related structure data
Related structure data | 5g32C 5g33C 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: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 5 / Auth seq-ID: 188 - 301 / Label seq-ID: 2 - 115
NCS oper:
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-Components
#1: Protein | Mass: 15612.728 Da / Num. of mol.: 2 / Fragment: UNP 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: 4722.201 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: 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 EIGER / Detector: PIXEL / Date: Nov 30, 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: 1.9→49.2 Å / Num. obs: 28204 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.4 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5A3D Resolution: 1.9→53.12 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.939 / SU B: 10.474 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.079 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→53.12 Å
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Refine LS restraints |
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