+Open data
-Basic information
Entry | Database: PDB / ID: 5a39 | ||||||
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Title | Structure of Rad14 in complex with cisplatin containing DNA | ||||||
Components |
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Keywords | REPLICATION / DNA REPAIR / DNA DAMAGE RECOGNITION / CISPLATIN | ||||||
Function / homology | Function and homology information nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair factor 1 complex / nucleotide-excision repair, DNA damage recognition / UV-damage excision repair / 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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Koch, S.C. / Kuper, J. / Gasteiger, K.L. / Wichlein, N. / Strasser, R. / Eisen, D. / Geiger, S. / 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 | 5a39.cif.gz | 211.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a39.ent.gz | 179.5 KB | Display | PDB format |
PDBx/mmJSON format | 5a39.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/5a39 ftp://data.pdbj.org/pub/pdb/validation_reports/a3/5a39 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.000733, 1, -0.000468), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 13673.528 Da / Num. of mol.: 2 / Fragment: DNA BINDING DOMAIN, UNP RESIDUES 188-302 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P28519 |
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-DNA chain , 3 types, 6 molecules CDEFGH
#2: DNA chain | Mass: 4519.947 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) #3: DNA chain | Mass: 4015.635 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) #4: DNA chain | Mass: 4040.647 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) |
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-Non-polymers , 2 types, 6 molecules
#5: Chemical | #6: Chemical | ChemComp-CPT / |
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-Details
Sequence details | CHAINS E,G AND CHAINS F,H DISPLAY MICROHETER |
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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: 2.15 Å3/Da / Density % sol: 42.74 % / Description: NONE |
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Crystal grow | Details: 0.2M MAGNESIUM ACETATE 0.1M MES PH 6.5 30% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.872 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 30, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.872 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→54.4 Å / Num. obs: 9402 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.33 / Mean I/σ(I) obs: 1.2 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NONE Resolution: 2.8→54.42 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.903 / SU B: 52.619 / SU ML: 0.475 / Cross valid method: THROUGHOUT / ESU R Free: 0.492 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED BIOMOLECULE IS COMPLETED BY CRYSTAL SYMMETRY
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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: 55.729 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→54.42 Å
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