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Open data
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Basic information
Entry | Database: PDB / ID: 1mwj | ||||||
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Title | Crystal Structure of a MUG-DNA pseudo substrate complex | ||||||
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![]() | HYDROLASE/DNA / Rossmann Fold / non-hydrolysable DNA-complex / Uracil recognition. / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | ![]() double-stranded uracil-DNA glycosylase / G/U mismatch-specific uracil-DNA glycosylase activity / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / base-excision repair, AP site formation / uracil DNA N-glycosylase activity / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Barrett, T.E. / Scharer, O. / Savva, R. / Brown, T. / Jiricny, J. / Verdine, G.L. / Pearl, L.H. | ||||||
![]() | ![]() Title: Crystal Structure of a thwarted mismatch glycosylase DNA repair complex Authors: Barrett, T.E. / Scharer, O. / Savva, R. / Brown, T. / Jiricny, J. / Verdine, G.L. / Pearl, L.H. | ||||||
History |
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Remark 300 | BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). The second strand of the DNA molecule is generated by applying symmetry operator 7_555 : y, x, -z, to DU and bases 8-12, and applying symmetry operator 7_554 : y, x, -1-z, to bases 1-6. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54.6 KB | Display | ![]() |
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PDB format | ![]() | 36.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 370.1 KB | Display | ![]() |
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Full document | ![]() | 372.7 KB | Display | |
Data in XML | ![]() | 5.2 KB | Display | |
Data in CIF | ![]() | 7.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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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
#1: DNA chain | Mass: 3665.365 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Protein | Mass: 18696.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0A9H1, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.78 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: microbatch / pH: 4.6 Details: PEG4000, Sodium Acetate, pH 4.6, Microbatch, temperature 289K | |||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: microdialysis / Details: Barrett, T.E., (1998) Cell., 92, 117. | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1998 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→20 Å / Num. all: 5478 / Num. obs: 5478 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.85→2.95 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 2 / Num. unique all: 472 / Rsym value: 0.263 / % possible all: 85.7 |
Reflection | *PLUS Num. obs: 5479 / Rmerge(I) obs: 0.087 |
Reflection shell | *PLUS % possible obs: 96.7 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 2.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Native MuG Resolution: 2.85→14.97 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 1104323.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: NO ELECTRON DENSITY IS OBSERVED FOR RESDUES 166 TO 168 RESIDUES A1, A109, A150 AND A151 WERE REFINED AS ALANINE
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Displacement parameters | Biso mean: 22.3 Å2 | ||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.35 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.38 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→14.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.85→2.93 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Rfactor obs: 0.23 / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.367 / Rfactor Rwork: 0.295 |