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- PDB-5omc: Crystal structure of K. lactis Ddc2 N-terminus in complex with S.... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5omc | ||||||
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Title | Crystal structure of K. lactis Ddc2 N-terminus in complex with S. cerevisiae Rfa1 (K45E mutant) N-OB domain | ||||||
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![]() | PROTEIN BINDING / Oligonucleotide-binding fold / coiled-coil domain / complex / mutant | ||||||
Function / homology | ![]() heteroduplex formation / sporulation / DNA replication factor A complex / Gap-filling DNA repair synthesis and ligation in GG-NER / telomere maintenance via telomere lengthening / Removal of the Flap Intermediate / telomere maintenance via recombination / Translesion Synthesis by POLH / Activation of the pre-replicative complex / Translesion synthesis by REV1 ...heteroduplex formation / sporulation / DNA replication factor A complex / Gap-filling DNA repair synthesis and ligation in GG-NER / telomere maintenance via telomere lengthening / Removal of the Flap Intermediate / telomere maintenance via recombination / Translesion Synthesis by POLH / Activation of the pre-replicative complex / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / single-stranded telomeric DNA binding / Activation of ATR in response to replication stress / mitotic recombination / Termination of translesion DNA synthesis / reciprocal meiotic recombination / DNA unwinding involved in DNA replication / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA topological change / Dual incision in TC-NER / telomere maintenance via telomerase / telomere maintenance / condensed nuclear chromosome / DNA damage checkpoint signaling / nucleotide-excision repair / double-strand break repair via homologous recombination / establishment of protein localization / chromatin organization / single-stranded DNA binding / double-stranded DNA binding / DNA replication / sequence-specific DNA binding / chromosome, telomeric region / damaged DNA binding / protein ubiquitination / DNA repair / mRNA binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Deshpande, I. / Seeber, A. / Shimada, K. / Keusch, J.J. / Gut, H. / Gasser, S.M. | ||||||
![]() | ![]() Title: Structural Basis of Mec1-Ddc2-RPA Assembly and Activation on Single-Stranded DNA at Sites of Damage. Authors: Deshpande, I. / Seeber, A. / Shimada, K. / Keusch, J.J. / Gut, H. / Gasser, S.M. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 192.9 KB | Display | ![]() |
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PDB format | ![]() | 156.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.6 KB | Display | ![]() |
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Full document | ![]() | 458.6 KB | Display | |
Data in XML | ![]() | 17.2 KB | Display | |
Data in CIF | ![]() | 23.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ombSC ![]() 5omdC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15382.277 Da / Num. of mol.: 2 / Fragment: UNP residues 1-132 / Mutation: K45E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: RFA1, BUF2, RPA1, YAR007C, FUN3 / Plasmid: pOPINF / Production host: ![]() ![]() #2: Protein | Mass: 12946.728 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M lithium sulfate monohydrate, 0.1 M Bis-Tris, 25% PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→50 Å / Num. obs: 21408 / % possible obs: 92.1 % / Redundancy: 3.77 % / Biso Wilson estimate: 56.98 Å2 / CC1/2: 0.993 / Rsym value: 0.139 / Net I/σ(I): 5.87 |
Reflection shell | Resolution: 2.38→2.45 Å / Redundancy: 2.92 % / Mean I/σ(I) obs: 0.99 / Num. unique obs: 1199 / CC1/2: 0.355 / Rsym value: 0.919 / % possible all: 69.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5OMB Resolution: 2.38→47.29 Å / Cor.coef. Fo:Fc: 0.9426 / Cor.coef. Fo:Fc free: 0.9021 / SU R Cruickshank DPI: 0.362 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.38 / SU Rfree Blow DPI: 0.265 / SU Rfree Cruickshank DPI: 0.264
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Displacement parameters | Biso mean: 57.13 Å2
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Refine analyze | Luzzati coordinate error obs: 0.345 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.38→47.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.38→2.5 Å / Total num. of bins used: 11
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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