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- PDB-2pax: THE CATALYTIC FRAGMENT OF POLY(ADP-RIBOSE) POLYMERASE COMPLEXED W... -

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Entry
Database: PDB / ID: 2pax
TitleTHE CATALYTIC FRAGMENT OF POLY(ADP-RIBOSE) POLYMERASE COMPLEXED WITH 4-AMINO-1,8-NAPHTHALIMIDE
ComponentsPOLY(ADP-RIBOSE) POLYMERASE
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE / NAD(+) ADP-RIBOSYLTRANSFERASE / DNA-BINDING
Function / homology
Function and homology information


NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / positive regulation of single strand break repair / NAD+-protein-serine 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-aspartate ADP-ribosyltransferase activity ...NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / positive regulation of single strand break repair / NAD+-protein-serine 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-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / NAD+-protein mono-ADP-ribosyltransferase activity / nuclear replication fork / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ poly-ADP-ribosyltransferase activity / positive regulation of double-strand break repair via homologous recombination / nucleosome binding / nucleotidyltransferase activity / negative regulation of innate immune response / 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
6-AMINO-BENZO[DE]ISOQUINOLINE-1,3-DIONE / Poly [ADP-ribose] polymerase 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 2.4 Å
AuthorsRuf, 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
DepositionNov 25, 1997Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_database_status / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 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)40,6282
Polymers40,4151
Non-polymers2121
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.230, 64.530, 96.410
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-4AN / 6-AMINO-BENZO[DE]ISOQUINOLINE-1,3-DIONE / 4-AMINO-1,8-NAPHTHALIMIDE


Mass: 212.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H8N2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsHUMAN SEQUENCE NUMBERS ARE USED THROUGHOUT INSTEAD OF CHICKEN NUMBERS TO FACILITATE COMPARISON WITH ...HUMAN SEQUENCE NUMBERS ARE USED THROUGHOUT INSTEAD OF CHICKEN NUMBERS TO FACILITATE COMPARISON WITH THE ABUNDANT LITERATURE ON HUMAN PARP. SUBTRACT 3 FOR RESPECTIVE CHICKEN NUMBERS.

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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 12% PEG 600, 6% ISOPROPANOL, 100 MM TRIS, PH 8.5 AND 0.03MM 4-AMINO-1,8-NAPHTALIMIDE
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.5 mg/mlprotein1drop
20.1 %(w/v)beta-octylglucoside1drop
35 mMAp4A1drop
417 %(w/v)PEG40001reservoir
58 %(v/v)2-propanol1reservoir
670 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.4→15.1 Å / Num. obs: 13590 / % possible obs: 94.9 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 13.8
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 7.3 / Rsym value: 0.232 / % possible all: 73.3
Reflection
*PLUS
% possible obs: 95 % / Num. measured all: 49815 / Rmerge(I) obs: 0.073
Reflection shell
*PLUS
% possible obs: 73 % / Rmerge(I) obs: 0.232

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 1PAX

1pax


Resolution: 2.4→15.1 Å / σ(F): 0 / Details: X-PLOR BULK SOLVENT CORRECTION WAS APPLIED.
RfactorNum. reflection% reflection
Rwork0.167 --
obs0.167 13590 94.9 %
Displacement parametersBiso mean: 35.8 Å2
Refine analyzeLuzzati sigma a obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.4→15.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2763 0 16 74 2853
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_d23.62
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.312
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.3
X-RAY DIFFRACTIONx_mcangle_it3.7
X-RAY DIFFRACTIONx_scbond_it4.2
X-RAY DIFFRACTIONx_scangle_it6.6
LS refinement shellResolution: 2.4→2.49 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rwork0.2716 750
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION3ANI.PARANI.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.62
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.312
LS refinement shell
*PLUS
Rfactor obs: 0.2716

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