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- PDB-1a26: THE CATALYTIC FRAGMENT OF POLY(ADP-RIBOSE) POLYMERASE COMPLEXED W... -

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Basic information

Entry
Database: PDB / ID: 1a26
TitleTHE CATALYTIC FRAGMENT OF POLY(ADP-RIBOSE) POLYMERASE COMPLEXED WITH CARBA-NAD
ComponentsPOLY (ADP-RIBOSE) POLYMERASE
KeywordsTRANSFERASE / 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 / replication fork reversal / ATP generation from poly-ADP-D-ribose / 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 / replication fork reversal / ATP generation from poly-ADP-D-ribose / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / nuclear replication fork / NAD+-protein ADP-ribosyltransferase activity / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleosome binding / positive regulation of double-strand break repair via homologous recombination / 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
Poly(ADP-ribose) polymerase, regulatory domain / Poly(ADP-ribose) Polymerase; domain 1 / Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / : / PADR1 domain, zinc ribbon fold / PADR1, N-terminal helical domain / PADR1 domain profile. / PADR1 ...Poly(ADP-ribose) polymerase, regulatory domain / Poly(ADP-ribose) Polymerase; domain 1 / Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / : / PADR1 domain, zinc ribbon fold / PADR1, N-terminal helical domain / PADR1 domain profile. / PADR1 / Zinc finger poly(ADP-ribose) polymerase (PARP)-type signature. / Zinc finger, PARP-type superfamily / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger poly(ADP-ribose) polymerase (PARP)-type profile. / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger, PARP-type / : / Poly(ADP-ribose) polymerase, regulatory domain / WGR domain / WGR domain superfamily / WGR domain / WGR domain profile. / Proposed nucleic acid binding domain / Poly(ADP-ribose) polymerase, regulatory domain superfamily / Poly(ADP-ribose) polymerase, regulatory domain / PARP alpha-helical domain profile. / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / BRCA1 C Terminus (BRCT) domain / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Poly [ADP-ribose] polymerase 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2.25 Å
AuthorsRuf, A. / Schulz, G.E.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: The mechanism of the elongation and branching reaction of poly(ADP-ribose) polymerase as derived from crystal structures and mutagenesis.
Authors: Ruf, A. / Rolli, V. / 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
DepositionJan 16, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.source / _pdbx_database_status.process_site
Revision 1.4Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: POLY (ADP-RIBOSE) POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0782
Polymers40,4151
Non-polymers6621
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.040, 64.440, 96.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein POLY (ADP-RIBOSE) POLYMERASE / PARP-CF / POLY(ADP-RIBOSE) TRANSFERASE / POLY (ADP-RIBOSE) SYNTHETASE


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
#2: Chemical ChemComp-CNA / CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 662.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H30N7O13P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 47 %
Crystal growpH: 8.5
Details: PROTEIN WAS CRYSTALLIZED FROM 10% PEG 600; 6% ISOPROPANOL, 100 MM TRIS PH 8.5, 5MM CARBA-NAD
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / Details: Jung, S., (1994) J.Mol.Biol., 244, 114.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.05 %(w/v)beta-OG1drop
23.75 mg/mlprotein1drop
32.5 mMAp4A1drop
48.5 %(w/v)PEG40001drop
54 %(v/v)2-propanol1drop
635 mMTris-HCl1drop
717 %(w/v)PEG40001reservoir
88 %(v/v)2-propanol1reservoir
970 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jul 24, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→23 Å / Num. obs: 16703 / % possible obs: 92.5 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 14.4
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 4 / Rsym value: 0.187 / % possible all: 63.3
Reflection
*PLUS
Num. measured all: 79881
Reflection shell
*PLUS
% possible obs: 63 % / Num. unique obs: 1089 / Num. measured obs: 2936

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
XSCALEdata scaling
X-PLORphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 1PAW

1paw
PDB Unreleased entry


Resolution: 2.25→22.6 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED
Cross valid method: THROUGHOUT, EXCEPT LAST REFINEMENT CYCLE
Details: THE X-PLOR BULK SOLVENT CORRECTION WAS USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1324 8 %RANDOM
Rwork0.168 ---
obs0.168 16703 92.5 %-
Displacement parametersBiso mean: 37 Å2
Refine analyzeLuzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.25→22.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2769 0 27 90 2886
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.3
X-RAY DIFFRACTIONx_mcangle_it3.6
X-RAY DIFFRACTIONx_scbond_it4.3
X-RAY DIFFRACTIONx_scangle_it6.7
LS refinement shellResolution: 2.25→2.29 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rwork0.278 563
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION3NAD.PARNAD.PAR
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.6

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