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

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Basic information

Entry
Database: PDB / ID: 5zdb
TitleCrystal structure of poly(ADP-ribose) glycohydrolase (PARG) from Deinococcus radiodurans in complex with ADP-ribose (P21)
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 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.972 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 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)56,3194
Polymers55,2002
Non-polymers1,1192
Water4,792266
1
A: Poly ADP-ribose glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1592
Polymers27,6001
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly ADP-ribose glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1592
Polymers27,6001
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.290, 97.427, 59.369
Angle α, β, γ (deg.)90.00, 93.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Poly ADP-ribose glycohydrolase


Mass: 27600.174 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (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.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M Sodium citrate tribasic dihydrate pH 6.0, 10% 2-Propanol, 10% Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.972→25.959 Å / Num. obs: 33944 / % possible obs: 98.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 14.353
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 2.019 / % possible all: 91.1

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZDA

5zda


Resolution: 1.972→25.959 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.81
RfactorNum. reflection% reflection
Rfree0.1967 2005 6.18 %
Rwork0.1551 --
obs0.1577 32431 93.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.972→25.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3873 0 72 266 4211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084041
X-RAY DIFFRACTIONf_angle_d0.9225509
X-RAY DIFFRACTIONf_dihedral_angle_d7.7592399
X-RAY DIFFRACTIONf_chiral_restr0.055603
X-RAY DIFFRACTIONf_plane_restr0.006733
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9723-2.02160.3098990.21031522X-RAY DIFFRACTION67
2.0216-2.07630.23861110.18331752X-RAY DIFFRACTION75
2.0763-2.13730.26191310.19311966X-RAY DIFFRACTION85
2.1373-2.20630.22331410.18452123X-RAY DIFFRACTION92
2.2063-2.28510.22611470.17332282X-RAY DIFFRACTION98
2.2851-2.37650.2281530.16842287X-RAY DIFFRACTION99
2.3765-2.48460.25221520.17192268X-RAY DIFFRACTION99
2.4846-2.61550.22161550.15832313X-RAY DIFFRACTION100
2.6155-2.77920.18271480.15492292X-RAY DIFFRACTION99
2.7792-2.99350.2231560.1532304X-RAY DIFFRACTION99
2.9935-3.29420.19071570.15162321X-RAY DIFFRACTION100
3.2942-3.76960.17131550.13812317X-RAY DIFFRACTION100
3.7696-4.74460.15091450.13252322X-RAY DIFFRACTION99
4.7446-25.96140.18131550.15652357X-RAY DIFFRACTION100
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)
11.5216-0.22240.36421.9346-0.18652.1811-0.0477-0.10310.00580.24640.0798-0.0371-0.00190.0209-0.03010.13610.01770.01330.1171-0.0080.138-3.1736-15.57185.6304
21.5537-0.3798-0.15281.5650.23911.3792-0.0319-0.0372-0.02080.20830.0468-0.04450.14820.0141-0.0030.13180.0048-0.01170.09710.01360.12780.3853-22.27444.0381
32.27-0.21810.01131.33190.28291.24930.00590.46840.3287-0.31560.0493-0.1359-0.14320.11880.01890.18870.00140.02350.22730.03180.20011.7756-11.7046-9.8132
41.82520.3631-0.49452.475-0.13942.7324-0.09790.0248-0.0507-0.2144-0.0095-0.11950.12970.07280.08340.15960.00510.01330.18140.02610.159518.6756-34.170538.1108
51.32540.0772-0.14892.2671-1.26232.2345-0.09720.3479-0.1537-0.49230.0016-0.14050.2385-0.07560.0770.2372-0.01070.02840.2319-0.01970.150316.1427-34.037928.3745
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 29:117 )A29 - 117
2X-RAY DIFFRACTION2( CHAIN A AND RESID 118:231 )A118 - 231
3X-RAY DIFFRACTION3( CHAIN A AND RESID 232:281 )A232 - 281
4X-RAY DIFFRACTION4( CHAIN B AND RESID 29:139 )B29 - 139
5X-RAY DIFFRACTION5( CHAIN B AND RESID 140:279 )B140 - 279

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