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- PDB-6oea: Crystal structure of HMCES SRAP domain in complex with longer 3' ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6oea | |||||||||
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Title | Crystal structure of HMCES SRAP domain in complex with longer 3' overhang DNA | |||||||||
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![]() | DNA BINDING PROTEIN/DNA / SRAP Domain / DNA-binding / Structural Genomics / Structural Genomics Consortium / SGC / HMCES / Protein-DNA complex / DNA damage protein / 3' overhang / DNA BINDING PROTEIN-DNA complex | |||||||||
Function / homology | ![]() protein-DNA covalent cross-linking activity / Lyases / DNA-(abasic site) binding / positive regulation of isotype switching / protein-DNA covalent cross-linking repair / Hydrolases; Acting on peptide bonds (peptidases) / double-strand break repair via alternative nonhomologous end joining / somatic hypermutation of immunoglobulin genes / interstrand cross-link repair / replication fork ...protein-DNA covalent cross-linking activity / Lyases / DNA-(abasic site) binding / positive regulation of isotype switching / protein-DNA covalent cross-linking repair / Hydrolases; Acting on peptide bonds (peptidases) / double-strand break repair via alternative nonhomologous end joining / somatic hypermutation of immunoglobulin genes / interstrand cross-link repair / replication fork / peptidase activity / single-stranded DNA binding / DNA damage response / proteolysis Similarity search - Function | |||||||||
Biological species | ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Halabelian, L. / Ravichandran, M. / Li, Y. / Zeng, H. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC) | |||||||||
![]() | ![]() Title: Structural basis of HMCES interactions with abasic DNA and multivalent substrate recognition. Authors: Halabelian, L. / Ravichandran, M. / Li, Y. / Zeng, H. / Rao, A. / Aravind, L. / Arrowsmith, C.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 | ![]() | 81.4 KB | Display | ![]() |
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PDB format | ![]() | 55 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5ko9SC ![]() 6oe7C ![]() 6oebC 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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1 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 31671.617 Da / Num. of mol.: 1 / Fragment: SRAP domain (UNP residues 2-270) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q96FZ2, Hydrolases; Acting on peptide bonds (peptidases) |
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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 3653.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 1840.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 62 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/UNX.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/UNX.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-UNX / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 20% PEG3350, 0.1 M potassium chloride, 0.1 M Bis-Tris, 0.05 M magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 18, 2018 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97741 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→49.11 Å / Num. obs: 25066 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.027 / Rrim(I) all: 0.069 / Net I/σ(I): 15 / Num. measured all: 165977 / Scaling rejects: 3 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 5KO9 Resolution: 2.1→49.16 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.2398 / WRfactor Rwork: 0.2016 / FOM work R set: 0.7085 / SU B: 7.002 / SU ML: 0.165 / SU R Cruickshank DPI: 0.1864 / SU Rfree: 0.1662 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.166 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 178.36 Å2 / Biso mean: 55.262 Å2 / Biso min: 34.72 Å2
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Refinement step | Cycle: final / Resolution: 2.1→49.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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