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- PDB-4a08: Structure of hsDDB1-drDDB2 bound to a 13 bp CPD-duplex (purine at... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4a08 | ||||||
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Title | Structure of hsDDB1-drDDB2 bound to a 13 bp CPD-duplex (purine at D-1 position) at 3.0 A resolution (CPD 1) | ||||||
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![]() | DNA-BINDING PROTEIN/DNA / DNA-BINDING PROTEIN-DNA COMPLEX / ![]() | ||||||
Function / homology | ![]() DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Dual Incision in GG-NER / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Scrima, A. / Fischer, E.S. / Iwai, S. / Gut, H. / Thoma, N.H. | ||||||
![]() | ![]() Title: The Molecular Basis of Crl4(Ddb2/Csa) Ubiquitin Ligase Architecture, Targeting, and Activation Authors: Scrima, A. / Fischer, E.S. / Iwai, S. / Gut, H. / Thoma, N.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 310.9 KB | Display | ![]() |
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PDB format | ![]() | 238.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4a09C ![]() 4a0aC ![]() 4a0bC ![]() 4a0cC ![]() 4a0kC ![]() 4a0lC ![]() 4a11C ![]() 3ei1S C: citing same article ( S: Starting model for refinement |
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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
-DNA DAMAGE-BINDING PROTEIN ... , 2 types, 2 molecules AB
#1: Protein | Mass: 129336.867 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 43418.102 Da / Num. of mol.: 1 / Fragment: RESIDUES 60-423 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
-DNA chain , 2 types, 2 molecules GH
#3: DNA chain | Mass: 4241.756 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: DAMAGED STRAND (CONTAINS CYCLOBUTANE PYRIMIDINE DIMER (TTD)) Source: (synth.) synthetic construct (others) |
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#4: DNA chain | Mass: 4273.753 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: UNDAMAGED STRAND / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 20 molecules ![](data/chem/img/MES.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
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#5: Chemical | ![]() #6: Chemical | #7: Water | ChemComp-HOH / | ![]() |
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-Details
Compound details | ENGINEEREDNonpolymer details | CYCLOBUTAN | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.78 % / Description: NONE |
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Crystal grow![]() | pH: 5.6 / Details: 100 MM MES, 25 MM NAOH, 18% PEG 350MME., pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3→50 Å / Num. obs: 37332 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 4.1 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 3EI1 Resolution: 3→48.62 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.841 / SU B: 21.52 / SU ML: 0.401 / Cross valid method: THROUGHOUT / ESU R Free: 0.52 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.672 Å2
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Refinement step | Cycle: LAST / Resolution: 3→48.62 Å
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Refine LS restraints |
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