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- PDB-5zde: Crystal structure of poly(ADP-ribose) glycohydrolase (PARG) from ... -

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Basic information

Entry
Database: PDB / ID: 5zde
TitleCrystal structure of poly(ADP-ribose) glycohydrolase (PARG) from Deinococcus radiodurans in complex with ADP-ribose (P3221)
ComponentsPoly ADP-ribose glycohydrolase
KeywordsHYDROLASE / ADP-ribose / poly(ADP-ribose) glycohydrolase
Function / homology
Function and homology information


Conserved hypothetical protein CHP02452 / Microbial-type PARG, catalytic domain / Microbial-type PARG, catalytic domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Macro domain-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-AR6 / Microbial-type PARG catalytic domain-containing protein
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCho, C.C. / Hsu, C.H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
National Science Council (Taiwan)105-2113-M-002-009 Taiwan
CitationJournal: Nat Commun / Year: 2019
Title: Structural and biochemical evidence supporting poly ADP-ribosylation in the bacterium Deinococcus radiodurans.
Authors: Cho, C.C. / Chien, C.Y. / Chiu, Y.C. / Lin, M.H. / Hsu, C.H.
History
DepositionFeb 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 9, 2025Group: 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 / entity / pdbx_entity_nonpoly / pdbx_entry_details
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.3Sep 17, 2025Group: Advisory / Derived calculations / Category: pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Poly ADP-ribose glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9492
Polymers27,3901
Non-polymers5591
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11010 Å2
Unit cell
Length a, b, c (Å)62.894, 62.894, 131.254
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"

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Components

#1: Protein Poly ADP-ribose glycohydrolase


Mass: 27389.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: DR_B0099 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9RZM4
#2: 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.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2
Has protein modificationN

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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: 2.71 Å3/Da / Density % sol: 54.53 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 20 % 2-Propanol, 20% Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.803→27.234 Å / Num. obs: 7430 / % possible obs: 99.9 % / Redundancy: 9.6 % / Biso Wilson estimate: 44.69 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 30.11

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Processing

Software
NameVersionClassification
phenix.refine1.13_2998refinement
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→27.23 Å / SU ML: 0.3471 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.3303 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2687 743 10 %
Rwork0.1816 6686 -
obs0.1903 7429 95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.33 Å2
Refinement stepCycle: LAST / Resolution: 2.8→27.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1913 0 36 0 1949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00931997
X-RAY DIFFRACTIONf_angle_d0.98782718
X-RAY DIFFRACTIONf_chiral_restr0.0502298
X-RAY DIFFRACTIONf_plane_restr0.0071361
X-RAY DIFFRACTIONf_dihedral_angle_d7.75691186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.020.34691160.22581029X-RAY DIFFRACTION74.74
3.02-3.320.29411520.22351371X-RAY DIFFRACTION99.93
3.32-3.80.29641500.1831386X-RAY DIFFRACTION100
3.8-4.790.23291600.15451409X-RAY DIFFRACTION99.94
4.79-27.240.25311650.17631491X-RAY DIFFRACTION99.88
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)
11.425933022540.2022007684110.2099782231310.9074468101980.2712552837440.3753179048170.186400913964-0.01317077520170.00250091419690.141404390955-0.2601352268370.2910016750440.0791928762328-0.7207895190350.0258123835235-0.00707797450337-0.0548385966513-0.03863803967780.874414498924-0.1714073473450.4262022825812.9783833402-4.7272598424213.689497037
21.75254908741-0.936491016319-0.2109841783582.52230545304-0.3483483175390.715218615360.1207113610540.450347521756-0.193519618118-0.36068802597-0.141902443453-0.2952132475420.0740784924903-0.03734443858660.06646341028970.1005386247950.06885887460340.03491003906370.524888097276-0.07717442705070.41808539390124.8783141638-5.943056898257.27060567138
30.4507742908350.0791836527326-0.2449796509171.229255485950.7894681831791.408629923550.04717260977280.0741299464656-0.0273599087999-0.175322022852-0.09818635676770.210217031040.169025504225-0.5360629777650.04281967024460.2414191963520.000603114495337-0.04431213789470.552865975098-0.09250101800270.30478230847717.4667380325-11.65592140216.91440421762
40.553930922099-0.396525374751-0.3674570435770.88058933875-0.2172752432310.663275008476-0.04664505649820.185210670947-0.28123060883-0.311723068203-0.1865045321410.8215219497460.495269254857-0.9124107576080.0657295242302-0.105426976908-0.314673443790.01706713334551.24489741598-0.3021616583740.5304131169116.37977260298-14.21406825215.3369847157
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 29 through 98 )
2X-RAY DIFFRACTION2chain 'C' and (resid 99 through 156 )
3X-RAY DIFFRACTION3chain 'C' and (resid 157 through 212 )
4X-RAY DIFFRACTION4chain 'C' and (resid 213 through 279 )

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