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- PDB-4n9y: Crystal structure of mouse poly(ADP-ribose) glycohydrolase (PARG)... -

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Basic information

Entry
Database: PDB / ID: 4n9y
TitleCrystal structure of mouse poly(ADP-ribose) glycohydrolase (PARG) catalytic domain mutant E748Q
ComponentsPoly(ADP-ribose) glycohydrolase
KeywordsHYDROLASE / Poly(ADP-ribose) glycohydrolase / PARG
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
Chem-V3L / Poly(ADP-ribose) glycohydrolase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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)61,2828
Polymers60,1471
Non-polymers1,1367
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.239, 91.103, 102.764
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Poly(ADP-ribose) glycohydrolase


Mass: 60146.598 Da / Num. of mol.: 1 / Fragment: mPARG catalytic domain / Mutation: E748Q
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.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-V3L / 2'-O-(5-O-phosphono-alpha-D-ribofuranosyl)adenosine 5'-(dihydrogen phosphate)


Type: RNA linking / Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.62 Å3/Da / Density % sol: 52.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / 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 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 2, 2012
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: 2.3→50 Å / Num. all: 27157 / Num. obs: 26481 / % possible obs: 97.51 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.114
Reflection shellResolution: 2.3→2.37 Å / % possible all: 90.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4FC2

4fc2


Resolution: 2.3→47.92 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.912 / Occupancy max: 1 / Occupancy min: 0.97 / SU B: 12.36 / SU ML: 0.154 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.329 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2398 1411 5.1 %RANDOM
Rwork0.1971 ---
obs0.1992 26480 97.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 75.3 Å2 / Biso mean: 31.2911 Å2 / Biso min: 10.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20 Å2
2---2.7 Å2-0 Å2
3---2.07 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4117 0 66 224 4407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0194283
X-RAY DIFFRACTIONr_bond_other_d0.0010.024022
X-RAY DIFFRACTIONr_angle_refined_deg1.1361.9765807
X-RAY DIFFRACTIONr_angle_other_deg0.73339260
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8575505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.75923.103203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47915737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4021536
X-RAY DIFFRACTIONr_chiral_restr0.0630.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214736
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021015
X-RAY DIFFRACTIONr_mcbond_it0.6071.8422026
X-RAY DIFFRACTIONr_mcbond_other0.6071.8412025
X-RAY DIFFRACTIONr_mcangle_it1.0592.762529
LS refinement shellResolution: 2.304→2.364 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 99 -
Rwork0.281 1637 -
all-1736 -
obs--83.3 %
Refinement TLS params.Method: refined / Origin x: -10.4053 Å / Origin y: 24.7481 Å / Origin z: -27.6161 Å
111213212223313233
T0.0472 Å2-0.0169 Å2-0.015 Å2-0.0139 Å20.0047 Å2--0.0453 Å2
L1.5446 °20.1704 °2-1.0312 °2-0.6189 °2-0.1305 °2--1.7513 °2
S0.0252 Å °-0.03 Å °-0.1633 Å °0.1106 Å °-0.0451 Å °0.046 Å °0.0982 Å °-0.0817 Å °0.02 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A442 - 956
2X-RAY DIFFRACTION1A1001 - 1007
3X-RAY DIFFRACTION1A1101 - 1324

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