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Yorodumi- PDB-3pax: THE CATALYTIC FRAGMENT OF POLY(ADP-RIBOSE) POLYMERASE COMPLEXED W... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pax | ||||||
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Title | THE CATALYTIC FRAGMENT OF POLY(ADP-RIBOSE) POLYMERASE COMPLEXED WITH 3-METHOXYBENZAMIDE | ||||||
Components | POLY(ADP-RIBOSE) POLYMERASE | ||||||
Keywords | TRANSFERASE / GLYCOSYLTRANSFERASE / NAD(+) ADP-RIBOSYLTRANSFERASE | ||||||
Function / homology | Function and homology information NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / NAD+-protein-serine ADP-ribosyltransferase activity / NAD+- protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / ATP generation from poly-ADP-D-ribose / replication fork reversal / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation ...NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / NAD+-protein-serine ADP-ribosyltransferase activity / NAD+- protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / ATP generation from poly-ADP-D-ribose / replication fork reversal / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / nuclear replication fork / NAD+-protein ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / positive regulation of double-strand break repair via homologous recombination / NAD+ ADP-ribosyltransferase activity / nucleosome binding / negative regulation of innate immune response / nucleotidyltransferase activity / NAD binding / double-strand break repair / site of double-strand break / damaged DNA binding / innate immune response / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 2.4 Å | ||||||
Authors | Ruf, A. / Schulz, G.E. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Inhibitor and NAD+ binding to poly(ADP-ribose) polymerase as derived from crystal structures and homology modeling. Authors: Ruf, A. / de Murcia, G. / Schulz, G.E. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1996 Title: Structure of the Catalytic Fragment of Poly(Ad-Ribose) Polymerase from Chicken Authors: Ruf, A. / Mennissier De Murcia, J. / De Murcia, G.M. / Schulz, G.E. #2: Journal: J.Mol.Biol. / Year: 1994 Title: Crystallization and X-Ray Crystallographic Analysis of Recombinant Chicken Poly(Adp-Ribose) Polymerase Catalytic Domain Produced in Sf9 Insect Cells Authors: Jung, S. / Miranda, E.A. / De Murcia, J.M. / Niedergang, C. / Delarue, M. / Schulz, G.E. / De Murcia, G.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pax.cif.gz | 82.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pax.ent.gz | 61.8 KB | Display | PDB format |
PDBx/mmJSON format | 3pax.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3pax_validation.pdf.gz | 430.4 KB | Display | wwPDB validaton report |
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Full document | 3pax_full_validation.pdf.gz | 433.7 KB | Display | |
Data in XML | 3pax_validation.xml.gz | 15 KB | Display | |
Data in CIF | 3pax_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pa/3pax ftp://data.pdbj.org/pub/pdb/validation_reports/pa/3pax | HTTPS FTP |
-Related structure data
Related structure data | 2pawC 2paxC 4paxC 1paxS 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: Protein | Mass: 40415.352 Da / Num. of mol.: 1 / Fragment: CATALYTIC FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Cell line: SF9 / Organelle: NUCLEUS / Plasmid: PVLPE / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P26446, NAD+ ADP-ribosyltransferase |
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#2: Chemical | ChemComp-3MB / |
#3: Water | ChemComp-HOH / |
Sequence details | HUMAN SEQUENCE NUMBERS ARE USED THROUGHOUT INSTEAD OF CHICKEN NUMBERS TO FACILITATE COMPARISON WITH ...HUMAN SEQUENCE NUMBERS ARE USED THROUGHOUT |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 47 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: PROTEIN WAS CRYSTALLIZED FROM 12% PEG 600, 6% ISOPROPANOL, 100 MM TRIS, PH 8.5, 5MM 3-METHOXYBENZAMIDE | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.98 |
Detector | Type: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Oct 18, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→19.8 Å / Num. obs: 15091 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.4→2.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.394 / % possible all: 100 |
Reflection | *PLUS % possible obs: 99 % / Num. measured all: 56084 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: PDB ENTRY 1PAX Resolution: 2.4→19.8 Å / Isotropic thermal model: RESTRAINED / Details: X-PLOR BULK SOLVENT CORRECTION WAS APPLIED.
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Displacement parameters | Biso mean: 35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→19.8 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |