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Yorodumi- PDB-5a3d: Structural insights into the recognition of cisplatin and AAF-dG ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5a3d | ||||||
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Title | Structural insights into the recognition of cisplatin and AAF-dG lesions by Rad14 (XPA) | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / XPA / RAD14 / NER / AAF-DG / CISPLATIN | ||||||
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: 1.8 Å | ||||||
Authors | Kuper, J. / Koch, S.C. / Gasteiger, K.L. / Wichlein, N. / Schneider, S. / Kisker, C. / Carell, T. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Structural Insights Into the Recognition of Cisplatin and Aaf-Dg Lesion by Rad14 (Xpa). Authors: Koch, S.C. / Kuper, J. / Gasteiger, K.L. / Simon, N. / Strasser, R. / Eisen, D. / Geiger, S. / Schneider, S. / Kisker, C. / Carell, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5a3d.cif.gz | 166 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a3d.ent.gz | 133.7 KB | Display | PDB format |
PDBx/mmJSON format | 5a3d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5a3d_validation.pdf.gz | 468.1 KB | Display | wwPDB validaton report |
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Full document | 5a3d_full_validation.pdf.gz | 491.8 KB | Display | |
Data in XML | 5a3d_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 5a3d_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/5a3d ftp://data.pdbj.org/pub/pdb/validation_reports/a3/5a3d | HTTPS FTP |
-Related 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 oper: (Code: given Matrix: (0.003171, -1, 0.001543), Vector: |
-Components
#1: Protein | Mass: 13673.528 Da / Num. of mol.: 2 / Fragment: DNA BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PPSG-IBA3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P28519 #2: DNA chain | | Mass: 4701.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) #3: DNA chain | | Mass: 5033.682 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | SYNTHESIZE | |
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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: 2.55 Å3/Da / Density % sol: 51.72 % / Description: NONE |
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Crystal grow | Details: 0.18 M AMMONIUM NITRATE AND 40% 2-METHYL- 1,3,-PROPANEDIOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97623 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97623 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→65.3 Å / Num. obs: 34232 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2.6 / % possible all: 95.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→53.73 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.424 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.138 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.76 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→53.73 Å
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Refine LS restraints |
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