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- PDB-1gs0: Crystal structure of the catalytic fragment of murine poly(ADP-ri... -

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Basic information

Entry
Database: PDB / ID: 1gs0
TitleCrystal structure of the catalytic fragment of murine poly(ADP-ribose) polymerase-2
ComponentsPOLY (ADP-RIBOSE) POLYMERASE-2
KeywordsTRANSFERASE / CATALYTIC FRAGMENT / POLYMERASE TRANSFERASE / NUCLEAR PROTEIN / DNA-BINDING
Function / homology
Function and homology information


NAD+-histone H2BE2 glutamate ADP-ribosyltransferase activity / NAD+-histone H2BE18 glutamate ADP-ribosyltransferase activity / HDR through MMEJ (alt-NHEJ) / POLB-Dependent Long Patch Base Excision Repair / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / response to oxygen-glucose deprivation / Formation of Incision Complex in GG-NER / hippocampal neuron apoptotic process / poly-ADP-D-ribose binding ...NAD+-histone H2BE2 glutamate ADP-ribosyltransferase activity / NAD+-histone H2BE18 glutamate ADP-ribosyltransferase activity / HDR through MMEJ (alt-NHEJ) / POLB-Dependent Long Patch Base Excision Repair / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / response to oxygen-glucose deprivation / Formation of Incision Complex in GG-NER / hippocampal neuron apoptotic process / poly-ADP-D-ribose binding / NAD+-histone H2BS6 serine ADP-ribosyltransferase activity / NAD+-histone H3S10 serine ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / positive regulation of cell growth involved in cardiac muscle cell development / NAD+-protein-serine ADP-ribosyltransferase activity / NAD DNA ADP-ribosyltransferase activity / DNA ADP-ribosylation / poly-ADP-D-ribose modification-dependent protein binding / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation / NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA repair-dependent chromatin remodeling / NAD+-protein mono-ADP-ribosyltransferase activity / site of DNA damage / NAD+ poly-ADP-ribosyltransferase activity / decidualization / Transferases; Glycosyltransferases; Pentosyltransferases / nucleosome binding / extrinsic apoptotic signaling pathway / nucleotidyltransferase activity / base-excision repair / damaged DNA binding / DNA repair / chromatin binding / nucleolus / nucleoplasm / nucleus
Similarity search - Function
Poly(ADP-ribose) polymerase, regulatory domain / Poly(ADP-ribose) Polymerase; domain 1 / : / 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 / Poly(ADP-ribose) Polymerase; domain 1 / : / 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 / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Poly [ADP-ribose] polymerase 2
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsOliver, A.W. / Roe, S.M. / Pearl, L.H.
CitationJournal: 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
DepositionDec 19, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: POLY (ADP-RIBOSE) POLYMERASE-2
B: POLY (ADP-RIBOSE) POLYMERASE-2


Theoretical massNumber of molelcules
Total (without water)79,3952
Polymers79,3952
Non-polymers00
Water1,35175
1
A: POLY (ADP-RIBOSE) POLYMERASE-2


Theoretical massNumber of molelcules
Total (without water)39,6981
Polymers39,6981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: POLY (ADP-RIBOSE) POLYMERASE-2


Theoretical massNumber of molelcules
Total (without water)39,6981
Polymers39,6981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)83.650, 85.820, 139.460
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-2 / PARP-2 / NAD(+) ADP-RIBOSYLTRANSFERASE-2 / POLY (ADP-RIBOSE) SYNTHETASE-2 / PADPRT-2


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 / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Compound detailsINVOLVED IN THE RESPONSE TO DNA DAMAGE.

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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: 3.3 Å3/Da / Density % sol: 62 %
Crystal growpH: 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
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
124 mg/mlprotein1drop
210 mMTris-HCl1droppH8.0
3100 mM1dropNaCl
49 %PEG80001reservoir
5100 mMTris-HCl1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9792
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EFY

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
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1225 4.8 %RANDOM
Rwork0.244 ---
obs0.244 25358 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.9173 Å2 / ksol: 0.3115 e/Å3
Displacement parametersBiso mean: 65.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.64 Å20 Å20 Å2
2--4.09 Å20 Å2
3----6.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5461 0 0 75 5536
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.439 201 4.8 %
Rwork0.403 3963 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79

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