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Yorodumi- PDB-1gs0: Crystal structure of the catalytic fragment of murine poly(ADP-ri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gs0 | ||||||
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Title | Crystal structure of the catalytic fragment of murine poly(ADP-ribose) polymerase-2 | ||||||
Components | POLY (ADP-RIBOSE) POLYMERASE-2Poly (ADP-ribose) polymerase | ||||||
Keywords | TRANSFERASE / CATALYTIC FRAGMENT / POLYMERASE TRANSFERASE / NUCLEAR PROTEIN / DNA-BINDING | ||||||
Function / homology | Function and homology information : / HDR through MMEJ (alt-NHEJ) / POLB-Dependent Long Patch Base Excision Repair / : / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / positive regulation of cell growth involved in cardiac muscle cell development / NAD DNA ADP-ribosyltransferase activity / DNA ADP-ribosylation ...: / HDR through MMEJ (alt-NHEJ) / POLB-Dependent Long Patch Base Excision Repair / : / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / positive regulation of cell growth involved in cardiac muscle cell development / NAD DNA ADP-ribosyltransferase activity / DNA ADP-ribosylation / NAD+ ADP-ribosyltransferase / protein poly-ADP-ribosylation / NAD+-protein ADP-ribosyltransferase activity / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / extrinsic apoptotic signaling pathway / base-excision repair / double-strand break repair / DNA repair / nucleolus / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Oliver, A.W. / Roe, S.M. / Pearl, L.H. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2004 Title: Crystal Structure of the Catalytic Fragment of Murine Poly(Adp-Ribose) Polymerase-2 Authors: Oliver, A.W. / Ame, J.C. / Roe, S.M. / Good, V. / De Murcia, G. / Pearl, L.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gs0.cif.gz | 145.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gs0.ent.gz | 114.7 KB | Display | PDB format |
PDBx/mmJSON format | 1gs0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gs/1gs0 ftp://data.pdbj.org/pub/pdb/validation_reports/gs/1gs0 | HTTPS FTP |
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-Related structure data
Related structure data | 1efyS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 39697.707 Da / Num. of mol.: 2 / Fragment: CATALYTIC FRAGMENT, RESIDUES 207-557 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: O88554, NAD+ ADP-ribosyltransferase #2: Water | ChemComp-HOH / | Compound details | INVOLVED IN THE RESPONSE TO DNA DAMAGE. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: 100 MM TRIS-HCL PH 8.0, 9% PEG 8000 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
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: ESRF / Beamline: ID14-4 / Wavelength: 0.9792 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 206775 / % possible obs: 99.9 % / Redundancy: 4 % / Biso Wilson estimate: 85 Å2 / Rsym value: 0.085 / Net I/σ(I): 4.2 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.255 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 25407 / Rmerge(I) obs: 0.073 |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.255 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EFY Resolution: 2.8→29.95 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 727909.41 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE LOOP CONTAINING RESIDUES 325 - 330 WAS NOT MODELLED DUE TO POOR ELECTRON DENSITY
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.9173 Å2 / ksol: 0.3115 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→29.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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