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

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Basic information

Entry
Database: PDB / ID: 5zdd
TitleCrystal structure of poly(ADP-ribose) glycohydrolase (PARG) from Deinococcus radiodurans in complex with ADP-ribose (P212121)
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 / PHOSPHATE ION / Microbial-type PARG catalytic domain-containing protein
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.725 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 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1573
Polymers27,5031
Non-polymers6542
Water543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-7 kcal/mol
Surface area11110 Å2
Unit cell
Length a, b, c (Å)42.713, 56.944, 97.451
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Poly ADP-ribose glycohydrolase


Mass: 27503.059 Da / Num. of mol.: 1
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.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.14 Å3/Da / Density % sol: 42.41 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
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: 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: 2.725→27.976 Å / Num. obs: 6555 / % possible obs: 98.6 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 13.623
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 2.868 / % possible all: 90.7

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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 / Resolution: 2.725→27.976 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.48
RfactorNum. reflection% reflection
Rfree0.2498 911 10.02 %
Rwork0.1617 --
obs0.1707 6555 74.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.725→27.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 5 3 1960
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012002
X-RAY DIFFRACTIONf_angle_d1.0792728
X-RAY DIFFRACTIONf_dihedral_angle_d7.7291188
X-RAY DIFFRACTIONf_chiral_restr0.053299
X-RAY DIFFRACTIONf_plane_restr0.007361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7254-2.86890.3806770.2473698X-RAY DIFFRACTION45
2.8689-3.04850.3171940.2755847X-RAY DIFFRACTION54
3.0485-3.28350.34171050.2139944X-RAY DIFFRACTION60
3.2835-3.61330.25561270.16991152X-RAY DIFFRACTION74
3.6133-4.13470.22661600.14281427X-RAY DIFFRACTION90
4.1347-5.20380.2271760.12991544X-RAY DIFFRACTION98
5.2038-27.97730.23111720.15191569X-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)
12.3713-2.41522.8115.6081-5.55387.74780.5604-1.2069-0.6698-1.34310.32251.13261.3124-1.3255-0.74180.3549-0.0757-0.03430.3385-0.01740.40786.2869-18.8886-16.5829
21.0632-0.0247-0.30044.48532.0054.7103-0.13381.2368-0.59070.3574-0.36380.88681.0191-0.9790.01530.32390.1335-0.0120.69290.08880.5189-4.29880.558-22.6032
38.5817-0.86020.37152.9176-0.24081.6742-0.6365-0.2160.42290.6860.4040.0361-0.353-0.26050.09130.3580.0197-0.0170.32660.02110.26076.08995.4867-5.7769
42.17370.47172.50982.659-1.1323.84770.13880.03460.01880.2099-0.167-0.34030.12260.4157-0.03420.2193-0.0153-0.05630.17430.02960.304713.721-6.7305-10.9564
51.92610.1697-0.5074.1011-0.78143.2784-0.35130.738-0.4129-0.23360.5499-0.74640.40551.02450.00150.33260.07490.0260.21940.00050.335414.4285-13.5849-21.1186
62.6172-0.50330.99492.7028-2.0522.33430.05250.0394-0.1525-0.1767-0.02980.02530.25960.1847-0.01030.19540.04440.05680.2192-0.08870.252513.6687-10.5703-15.8415
72.20830.5538-1.35942.1396-2.07022.7757-0.03940.28610.20280.0178-0.0024-0.0215-0.1087-0.18790.00570.27550.0005-0.00290.2703-0.00250.23312.12981.3273-22.0597
85.59080.5396-0.67352.269-0.30762.81110.059-0.25390.59720.17490.06180.0005-0.55310.1626-0.01470.3738-0.00280.0090.2760.01430.40413.19479.3459-10.8509
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 45 )
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 59 )
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 73 )
4X-RAY DIFFRACTION4chain 'A' and (resid 74 through 109 )
5X-RAY DIFFRACTION5chain 'A' and (resid 110 through 137 )
6X-RAY DIFFRACTION6chain 'A' and (resid 138 through 168 )
7X-RAY DIFFRACTION7chain 'A' and (resid 169 through 231 )
8X-RAY DIFFRACTION8chain 'A' and (resid 232 through 280 )

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