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- PDB-4n9z: Crystal structure of mouse poly(ADP-ribose) glycohydrolase (PARG)... -

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Basic information

Entry
Database: PDB / ID: 4n9z
TitleCrystal structure of mouse poly(ADP-ribose) glycohydrolase (PARG) catalytic domain mutant E749Q
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: 1.9 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)122,37214
Polymers120,2932
Non-polymers2,07912
Water17,421967
1
A: Poly(ADP-ribose) glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1867
Polymers60,1471
Non-polymers1,0406
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Poly(ADP-ribose) glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1867
Polymers60,1471
Non-polymers1,0406
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.915, 91.283, 102.522
Angle α, β, γ (deg.)90.000, 91.200, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Poly(ADP-ribose) glycohydrolase


Mass: 60146.598 Da / Num. of mol.: 2 / Fragment: catalytic domain / Mutation: E749Q
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-V3L / 2'-O-(5-O-phosphono-alpha-D-ribofuranosyl)adenosine 5'-(dihydrogen phosphate)


Type: RNA linking / Mass: 559.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 967 / 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: 2.6 Å3/Da / Density % sol: 52.73 %
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: 1.9→29.88 Å / Num. all: 96469 / Num. obs: 95128 / % possible obs: 98.61 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Rmerge(I) obs: 0.11
Reflection shellResolution: 1.9→1.96 Å

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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: 1.9→29.88 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 0.97 / SU B: 5.647 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 4773 5 %RANDOM
Rwork0.1901 ---
obs0.1921 95110 98.61 %-
all-96451 --
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: 95 Å2 / Biso mean: 20.0806 Å2 / Biso min: 6.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å2-0 Å20.45 Å2
2---1 Å2-0 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8251 0 122 967 9340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198575
X-RAY DIFFRACTIONr_bond_other_d0.0010.028063
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.97511626
X-RAY DIFFRACTIONr_angle_other_deg0.792318562
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.07851013
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83523.103406
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.258151475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4281572
X-RAY DIFFRACTIONr_chiral_restr0.0790.21256
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219493
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022033
X-RAY DIFFRACTIONr_mcbond_it1.3972.3254064
X-RAY DIFFRACTIONr_mcbond_other1.3962.3234063
X-RAY DIFFRACTIONr_mcangle_it2.0813.8955073
LS refinement shellResolution: 1.904→1.953 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 333 -
Rwork0.216 6206 -
all-6539 -
obs--92.29 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0649-0.1749-0.86860.450.11671.43790.0002-0.0246-0.0887-0.0603-0.0159-0.01110.08320.08430.01570.03080.009-0.0230.01910.00140.044523.8871-95.2785129.5114
20.9113-0.14640.5310.4033-0.03671.22490.0349-0.00250.0864-0.0576-0.02460.0001-0.1116-0.0937-0.01020.02910.02070.00230.0353-0.00280.03163.2713-53.5739129.736
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A442 - 957
2X-RAY DIFFRACTION1A1001 - 1006
3X-RAY DIFFRACTION1A1101 - 1538
4X-RAY DIFFRACTION2B442 - 957
5X-RAY DIFFRACTION2B1001 - 1006
6X-RAY DIFFRACTION2B1101 - 1629

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