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- PDB-4na5: Crystal structure of mouse poly(ADP-ribose) glycohydrolase (PARG)... -

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Basic information

Entry
Database: PDB / ID: 4na5
TitleCrystal structure of mouse poly(ADP-ribose) glycohydrolase (PARG) catalytic domain mutant E748N
ComponentsPoly(ADP-ribose) glycohydrolase
KeywordsHYDROLASE / Poly(ADP-ribose) glycohydrolase
Function / homology
Function and homology information


POLB-Dependent Long Patch Base Excision Repair / poly(ADP-ribose) glycohydrolase activity / poly(ADP-ribose) glycohydrolase / ATP generation from poly-ADP-D-ribose / detection of bacterium / regulation of DNA repair / carbohydrate metabolic process / DNA damage response / nucleus / cytosol
Similarity search - Function
Poly(ADP-ribose) glycohydrolase / Poly (ADP-ribose) glycohydrolase (PARG), catalytic domain / : / Poly (ADP-ribose) glycohydrolase (PARG), Macro domain fold / Poly (ADP-ribose) glycohydrolase (PARG), helical domain
Similarity search - Domain/homology
Poly(ADP-ribose) glycohydrolase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, Z. / Cheng, Z. / Xu, W.
CitationJournal: Plos One / Year: 2014
Title: Crystallographic and biochemical analysis of the mouse poly(ADP-ribose) glycohydrolase.
Authors: Wang, Z. / Gagne, J.P. / Poirier, G.G. / Xu, W.
History
DepositionOct 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poly(ADP-ribose) glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5175
Polymers60,1331
Non-polymers3844
Water7,332407
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.091, 91.293, 103.504
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Poly(ADP-ribose) glycohydrolase


Mass: 60132.574 Da / Num. of mol.: 1 / Fragment: catalytic domain / Mutation: E748N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Parg / Production host: Escherichia coli (E. coli)
References: UniProt: O88622, poly(ADP-ribose) glycohydrolase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.64 Å3/Da / Density % sol: 53.33 %
Crystal growTemperature: 277 K / pH: 6
Details: 0.2M (NH4)2SO4, 16% PEG3,350, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 43475 / % possible obs: 99.3 % / Observed criterion σ(I): 1.5
Reflection shellResolution: 2→2.06 Å / % possible all: 92.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0110refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.405 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.214 2189 5.1 %RANDOM
Rwork0.18 ---
obs0.182 43291 98.8 %-
all-43826 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4097 0 20 407 4524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224214
X-RAY DIFFRACTIONr_bond_other_d0.0010.022960
X-RAY DIFFRACTIONr_angle_refined_deg1.1381.9635704
X-RAY DIFFRACTIONr_angle_other_deg0.84337158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9525502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.04223.085201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17315734
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8141536
X-RAY DIFFRACTIONr_chiral_restr0.070.2612
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214618
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02897
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.40942522
X-RAY DIFFRACTIONr_mcbond_other0.4441012
X-RAY DIFFRACTIONr_mcangle_it2.17764083
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.79461692
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.271101621
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 142 -
Rwork0.271 2708 -
obs--89.59 %
Refinement TLS params.Method: refined / Origin x: 9.9947 Å / Origin y: -66.3324 Å / Origin z: 131.2729 Å
111213212223313233
T0.0598 Å20.0246 Å2-0.0172 Å2-0.0165 Å20.0033 Å2--0.0711 Å2
L1.328 °2-0.149 °2-0.9233 °2-0.5716 °20.0871 °2--1.6731 °2
S0.0146 Å °0.002 Å °-0.1472 Å °-0.1147 Å °-0.0504 Å °-0.0474 Å °0.1266 Å °0.1045 Å °0.0358 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A442 - 956
2X-RAY DIFFRACTION1A1001 - 1004
3X-RAY DIFFRACTION1A1101 - 1507

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