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- PDB-5zdg: Crystal structure of poly(ADP-ribose) glycohydrolase (PARG) T267R... -

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Basic information

Entry
Database: PDB / ID: 5zdg
TitleCrystal structure of poly(ADP-ribose) glycohydrolase (PARG) T267R mutant from Deinococcus radiodurans in complex with ADP-ribose
ComponentsPoly APD-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: 2.594 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Poly APD-ribose glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0052
Polymers27,4461
Non-polymers5591
Water1448
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 area10950 Å2
Unit cell
Length a, b, c (Å)63.044, 63.044, 130.976
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11C-406-

HOH

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Components

#1: Protein Poly APD-ribose glycohydrolase


Mass: 27445.988 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.76 Å3/Da / Density % sol: 55.44 %
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, 10 mM Hexammine cobalt (lll) chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 2.59375→28.4029 Å / Num. obs: 8901 / % possible obs: 99.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 29.84
Reflection shellResolution: 3.53→3.88 Å / Rmerge(I) obs: 0.579

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.594→28.4029 Å / SU ML: 0.239169240224 / Cross valid method: THROUGHOUT / σ(F): 1.34358811396 / Phase error: 26.5266437295
RfactorNum. reflection% reflection
Rfree0.251134062422 1195 10.0310585075 %
Rwork0.185624568988 --
obs0.192261801375 8901 66.0402461334 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 51.4907629656 Å2
Refinement stepCycle: LAST / Resolution: 2.594→28.4029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1917 0 36 8 1961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008728457407452000
X-RAY DIFFRACTIONf_angle_d1.025808586372722
X-RAY DIFFRACTIONf_chiral_restr0.0525361158797297
X-RAY DIFFRACTIONf_plane_restr0.00575047750897362
X-RAY DIFFRACTIONf_dihedral_angle_d7.74334430161190
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5938-2.69750.349744427322450.245941913354447X-RAY DIFFRACTION24.9366447035
2.6975-2.82020.28379683264850.22942601398705X-RAY DIFFRACTION38.9546351085
2.8202-2.96870.3116509507251050.2447915130021008X-RAY DIFFRACTION55.9296482412
2.9687-3.15450.2815967930411280.2532324467481099X-RAY DIFFRACTION59.8536585366
3.1545-3.39770.301511383111290.2186693356671097X-RAY DIFFRACTION62.5510204082
3.3977-3.73890.2516663874241300.2056269977071207X-RAY DIFFRACTION66.024691358
3.7389-4.27840.2438977652981620.1558042372091564X-RAY DIFFRACTION86.4296444667
4.2784-5.38430.2310687043152040.1612734308851793X-RAY DIFFRACTION99.7502497502
5.3843-28.40460.2323196735172070.1760236508641798X-RAY DIFFRACTION99.7512437811
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)
12.850516776920.105267809703-0.05148098638343.1365833044-1.450209774253.129224423190.221399859337-0.04641483112290.2192300050220.149938109614-0.31217116109-0.365342417093-0.2917091505390.63230795277-0.04090624520470.20771031388-0.03013042405680.0467459836020.5088032783410.06988069487220.35422292095117.599124389860.777024711616.9460165595
21.842995559060.5958296576450.6304395148792.75359800869-0.6626654638072.416268767170.2731801924670.2347458959560.00586588022156-0.665115307882-0.2602973189560.1161952398140.07557731529350.3640209132240.02283724360720.2392052412180.05310552965780.01726356421010.5174392576830.03011696351570.30652240432811.329828430858.24483269296.20402012382
30.530973426980.2442485860260.5055006162412.27495183186-2.329140617993.136389063380.1576077881870.296002670967-0.005057506740030.0988572423945-0.25577903089-0.0643357605878-0.2429901947750.4583258547320.03532882379450.1234523226010.04730182195210.04227069436350.5405125488750.06738941665810.32324441603512.830576952665.67352949067.97006077542
42.76330628443-0.5000303623010.1671139252882.781338676130.4372675155271.372476820320.0303205509450.2707812580730.447838823221-0.60309411214-0.224808361065-0.885444471776-1.19284143731.08840404789-0.0219304740290.242322122461-0.2130410679860.05422605884431.016918398960.1905827327320.55774321935525.098163944968.87418751225.33921797868
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 29 through 73 )
2X-RAY DIFFRACTION2chain 'C' and (resid 74 through 139 )
3X-RAY DIFFRACTION3chain 'C' and (resid 140 through 212 )
4X-RAY DIFFRACTION4chain 'C' and (resid 213 through 279 )

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