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- PDB-4na0: Crystal structure of mouse poly(ADP-ribose) glycohydrolase (PARG)... -

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Basic information

Entry
Database: PDB / ID: 4na0
TitleCrystal structure of mouse poly(ADP-ribose) glycohydrolase (PARG) catalytic domain with ADPRibose
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
Chem-AR6 / IODIDE ION / Poly(ADP-ribose) glycohydrolase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement-SAD / Resolution: 2.4 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 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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
C: Poly(ADP-ribose) glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,14812
Polymers181,7093
Non-polymers2,4399
Water00
1
A: Poly(ADP-ribose) glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3834
Polymers60,5701
Non-polymers8133
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Poly(ADP-ribose) glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3834
Polymers60,5701
Non-polymers8133
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Poly(ADP-ribose) glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3834
Polymers60,5701
Non-polymers8133
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)188.300, 55.665, 166.149
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: 60569.629 Da / Num. of mol.: 3 / Fragment: catalytic domain
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-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H23N5O14P2
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.22M KI 20% PEG3,350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2011
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 68770 / Num. obs: 67670 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.113
Reflection shellResolution: 2.4→2.47 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0110refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: molecular replacement-SAD / Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.901 / Occupancy max: 1 / Occupancy min: 1 / SU B: 34.856 / SU ML: 0.379 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.673 / ESU R Free: 0.37 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3419 3412 5.1 %RANDOM
Rwork0.2977 ---
all0.2999 69049 --
obs0.2999 67440 97.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 290.86 Å2 / Biso mean: 70.4119 Å2 / Biso min: 16.68 Å2
Baniso -1Baniso -2Baniso -3
1--3.03 Å20 Å20 Å2
2--0.41 Å20 Å2
3---2.62 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12223 0 114 0 12337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02212641
X-RAY DIFFRACTIONr_bond_other_d0.0010.028851
X-RAY DIFFRACTIONr_angle_refined_deg1.3461.9717133
X-RAY DIFFRACTIONr_angle_other_deg0.983321412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.94151494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.80623.069606
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.959152190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.61815108
X-RAY DIFFRACTIONr_chiral_restr0.0750.21847
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02113822
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022702
X-RAY DIFFRACTIONr_mcbond_it1.12647503
X-RAY DIFFRACTIONr_mcbond_other0.25543012
X-RAY DIFFRACTIONr_mcangle_it1.905612131
X-RAY DIFFRACTIONr_scbond_it2.23665138
X-RAY DIFFRACTIONr_scangle_it3.405104993
LS refinement shellResolution: 2.404→2.467 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.439 213 -
Rwork0.379 4237 -
all-4450 -
obs--88.96 %
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)
17.6408-1.2561-0.90832.9723-0.17021.0743-0.4084-0.60690.21050.45080.3836-0.09290.0977-0.09960.02480.35990.17880.01390.1641-0.02760.021663.832934.952498.4311
212.2053-0.4768-1.19081.68330.35391.4726-0.25681.0171-0.4362-0.17250.1110.26250.115-0.13220.14580.38540.09250.05610.1750.00460.069130.82166.2468123.0913
314.3159-3.9504-1.68022.79640.38691.3278-0.6776-1.514-0.30160.54740.57190.02730.14430.18560.10570.40220.12950.070.20770.01650.034563.801534.9404153.8672
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A444 - 956
2X-RAY DIFFRACTION1A1001 - 1003
3X-RAY DIFFRACTION2B444 - 955
4X-RAY DIFFRACTION2B1001 - 1003
5X-RAY DIFFRACTION3C444 - 956
6X-RAY DIFFRACTION3C1001 - 1003

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