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

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Basic information

Entry
Database: PDB / ID: 5zda
TitleCrystal structure of poly(ADP-ribose) glycohydrolase (PARG) from Deinococcus radiodurans in apo form
Componentspoly ADP-ribose glycohydrolase
KeywordsHYDROLASE / ADP-ribose / poly(ADP-ribose) glycohydrolase
Function / homologyConserved 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 / Microbial-type PARG catalytic domain-containing protein
Function and homology information
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.548 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 / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8502
Polymers27,7541
Non-polymers961
Water5,134285
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-10 kcal/mol
Surface area11890 Å2
Unit cell
Length a, b, c (Å)45.096, 71.073, 72.257
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: 27754.340 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.16 Å3/Da / Density % sol: 43.04 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2M Li2SO4, 0.1 M Bis-Tris pH 6.5, 25% PEG 3350

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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: Nov 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.548→26.21 Å / Num. obs: 33721 / % possible obs: 97.66 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 19.53
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 4.391 / % possible all: 100

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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: 3SIH

3sih


Resolution: 1.548→26.209 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.27
RfactorNum. reflection% reflection
Rfree0.1899 1989 5.9 %
Rwork0.1696 --
obs0.1708 33710 97.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.548→26.209 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1888 0 5 285 2178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061961
X-RAY DIFFRACTIONf_angle_d0.8132674
X-RAY DIFFRACTIONf_dihedral_angle_d5.1851635
X-RAY DIFFRACTIONf_chiral_restr0.051293
X-RAY DIFFRACTIONf_plane_restr0.007362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5482-1.58690.25651390.19862223X-RAY DIFFRACTION98
1.5869-1.62980.20971420.18892281X-RAY DIFFRACTION100
1.6298-1.67780.22581450.18922305X-RAY DIFFRACTION100
1.6778-1.73190.20441430.18612286X-RAY DIFFRACTION100
1.7319-1.79380.21171460.17672282X-RAY DIFFRACTION100
1.7938-1.86560.22061460.16612291X-RAY DIFFRACTION100
1.8656-1.95050.19291310.18042158X-RAY DIFFRACTION93
1.9505-2.05330.1991480.16982303X-RAY DIFFRACTION100
2.0533-2.18190.18711400.17072313X-RAY DIFFRACTION100
2.1819-2.35020.19941210.16641862X-RAY DIFFRACTION81
2.3502-2.58650.20371430.17062330X-RAY DIFFRACTION100
2.5865-2.96040.20211470.18182346X-RAY DIFFRACTION100
2.9604-3.72810.18231420.15932283X-RAY DIFFRACTION96
3.7281-26.21250.15761560.15952458X-RAY DIFFRACTION99
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)
10.5833-0.0991-0.15363.160.49420.7419-0.0413-0.0326-0.0645-0.14450.0980.59660.0542-0.1539-0.08740.1406-0.0173-0.02010.2090.01410.2255-14.354524.341714.7055
21.88460.4196-0.23322.1590.42090.78710.02240.0537-0.0258-0.3868-0.0428-0.03870.0279-0.14350.00630.19020.0154-0.01220.1492-0.00450.1056-0.075820.33863.6946
31.00310.4805-0.28292.3642-1.93823.3765-0.0131-0.3673-0.06180.8447-0.092-0.5476-0.43130.6940.06090.2987-0.0027-0.05710.26880.01070.24571.905832.073619.3394
42.6937-0.1097-0.83374.1171-0.7741.12720.0158-0.40550.00880.60880.00110.2492-0.15920.0327-0.00580.2039-0.00310.02380.2046-0.01560.1388-8.431230.595725.0571
51.3882-0.07910.00712.2605-0.34691.116-0.0052-0.07130.04890.06280.0902-0.01270.0007-0.0388-0.0650.10660.0075-0.00220.1078-0.0380.0969-0.692927.40817.2592
60.8343-0.4005-0.10291.9045-0.271.3099-0.0236-0.035-0.04540.0086-0.0285-0.04790.01090.05110.03990.1083-0.0102-0.00350.1219-0.00170.1182.098414.449515.4777
74.19551.1243-0.0595.2570.17132.8065-0.03340.209-0.3236-0.3128-0.0216-0.2390.20860.21170.02190.14420.0220.0410.15250.01430.145310.827410.40057.5173
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 59 )
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 93 )
3X-RAY DIFFRACTION3chain 'A' and (resid 94 through 119 )
4X-RAY DIFFRACTION4chain 'A' and (resid 120 through 139 )
5X-RAY DIFFRACTION5chain 'A' and (resid 140 through 188 )
6X-RAY DIFFRACTION6chain 'A' and (resid 189 through 265 )
7X-RAY DIFFRACTION7chain 'A' and (resid 266 through 281 )

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