+Open data
-Basic information
Entry | Database: PDB / ID: 1ssp | ||||||
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Title | WILD-TYPE URACIL-DNA GLYCOSYLASE BOUND TO URACIL-CONTAINING DNA | ||||||
Components |
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Keywords | HYDROLASE/DNA / DNA GLYCOSYLASE / DNA BASE EXCISION REPAIR / URACIL / DNA / PROTEIN/DNA / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / isotype switching / uracil DNA N-glycosylase activity / ribosomal small subunit binding / somatic hypermutation of immunoglobulin genes / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine ...base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / isotype switching / uracil DNA N-glycosylase activity / ribosomal small subunit binding / somatic hypermutation of immunoglobulin genes / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Chromatin modifications during the maternal to zygotic transition (MZT) / base-excision repair / damaged DNA binding / negative regulation of apoptotic process / mitochondrion / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Parikh, S.S. / Mol, C.D. / Slupphaug, G. / Bharati, S. / Krokan, H.E. / Tainer, J.A. | ||||||
Citation | Journal: EMBO J. / Year: 1998 Title: Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA. Authors: Parikh, S.S. / Mol, C.D. / Slupphaug, G. / Bharati, S. / Krokan, H.E. / Tainer, J.A. #1: Journal: Nature / Year: 1996 Title: A Nucleotide-Flipping Mechanism from the Structure of Human Uracil-DNA Glycosylase Bound to DNA Authors: Slupphaug, G. / Mol, C.D. / Kavli, B. / Arvai, A.S. / Krokan, H.E. / Tainer, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ssp.cif.gz | 71.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ssp.ent.gz | 53.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ssp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ss/1ssp ftp://data.pdbj.org/pub/pdb/validation_reports/ss/1ssp | HTTPS FTP |
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-Related structure data
Related structure data | 1akzSC 2sspC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 2892.878 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3399.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: COMPLEXED WITH URACIL |
#3: Protein | Mass: 25544.137 Da / Num. of mol.: 1 / Fragment: MITOCHONDRIAL Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P13051, uridine nucleosidase |
#4: Chemical | ChemComp-URA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% PEG 4000, 100 MM HEPES PH 6.5, 10% DIOXANE, 1 MM DITHIOTHREITOL, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Date: Apr 19, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 30394 / % possible obs: 97.5 % / Redundancy: 3.3 % / Rsym value: 0.06 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.9→1.97 Å / Mean I/σ(I) obs: 4.2 / Rsym value: 0.212 / % possible all: 87.1 |
Reflection | *PLUS Num. measured all: 105498 / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS % possible obs: 87.1 % / Rmerge(I) obs: 0.212 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AKZ Resolution: 1.9→20 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.99 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Num. reflection obs: 30363 / σ(F): 2 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.292 / Rfactor Rwork: 0.268 |