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- PDB-5zdf: Crystal structure of poly(ADP-ribose) glycohydrolase (PARG) T267K... -

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Basic information

Entry
Database: PDB / ID: 5zdf
TitleCrystal structure of poly(ADP-ribose) glycohydrolase (PARG) T267K mutant from Deinococcus radiodurans in complex with ADP-ribose
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: 2.504 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)27,9772
Polymers27,4181
Non-polymers5591
Water43224
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 area11080 Å2
Unit cell
Length a, b, c (Å)63.176, 63.176, 130.929
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-410-

HOH

21A-416-

HOH

31A-420-

HOH

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Components

#1: Protein Poly ADP-ribose glycohydrolase


Mass: 27417.975 Da / Num. of mol.: 1 / Mutation: T267K
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.: 24 / 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: 2.77 Å3/Da / Density % sol: 55.66 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.2, 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: 2.504→28.449 Å / Num. obs: 10823 / % possible obs: 98.8 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.147 / Net I/σ(I): 15.4
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 2.259 / % possible all: 90.4

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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: 2.504→28.449 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.33
RfactorNum. reflection% reflection
Rfree0.2487 1541 9.96 %
Rwork0.1994 --
obs0.2044 9874 76.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.504→28.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1915 0 36 24 1975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091997
X-RAY DIFFRACTIONf_angle_d1.052719
X-RAY DIFFRACTIONf_dihedral_angle_d8.2711189
X-RAY DIFFRACTIONf_chiral_restr0.05297
X-RAY DIFFRACTIONf_plane_restr0.007361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5042-2.5850.2772610.259508X-RAY DIFFRACTION31
2.585-2.67730.2505830.2717661X-RAY DIFFRACTION41
2.6773-2.78450.3399950.2652915X-RAY DIFFRACTION55
2.7845-2.91110.28591030.24451081X-RAY DIFFRACTION65
2.9111-3.06440.26641350.24431164X-RAY DIFFRACTION72
3.0644-3.25610.31691530.24641388X-RAY DIFFRACTION84
3.2561-3.50710.30951820.21961636X-RAY DIFFRACTION97
3.5071-3.85930.24271880.19311623X-RAY DIFFRACTION100
3.8593-4.41590.22551750.16781663X-RAY DIFFRACTION100
4.4159-5.55680.20881860.17431641X-RAY DIFFRACTION100
5.5568-28.45110.2191800.17821647X-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)
16.54432.8219-2.3441.2491-0.872.1505-0.1648-0.3468-0.3018-0.1799-0.0883-0.24460.0937-0.17960.27790.4560.19540.02420.33320.01340.36438.5428-22.8542-14.2799
21.61550.0238-0.25461.58080.88792.1644-0.5192-0.08830.6002-0.30380.05940.1813-1.0645-0.16450.23480.92760.3991-0.18390.4023-0.14490.481410.3792-3.38-14.2444
35.6431-0.7351-0.723.5969-0.23610.3999-0.1893-1.1455-0.14710.84910.0513-0.2626-0.01290.00730.16350.59850.3006-0.00480.48990.04110.296114.4934-19.4342-3.425
42.74531.35931.07561.44120.26151.91780.0103-0.7789-0.1550.0086-0.1029-0.0061-0.1044-0.30.12040.47780.2814-0.02540.488-0.0260.343113.9166-16.5206-8.0332
53.43411.50452.75990.90591.14393.7431-0.0586-0.02640.334-0.5120.1869-0.0262-0.5530.40420.05320.6040.1405-0.02890.2325-0.02740.239628.1537-6.4759-8.7142
62.197-0.42340.02611.3996-0.64191.3079-0.0704-0.87191.00910.2047-0.31280.1542-1.56360.32260.31561.17640.5458-0.2789-0.0151-0.03920.567715.7605-0.0394-6.4264
71.62280.6697-1.7864.1641.38913.70490.13210.19620.7456-0.8502-0.04930.3898-0.8829-0.3412-0.0111.41810.3519-0.36010.6713-0.24540.917914.98737.506-1.1559
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 93 )
3X-RAY DIFFRACTION3chain 'A' and (resid 94 through 129 )
4X-RAY DIFFRACTION4chain 'A' and (resid 130 through 176 )
5X-RAY DIFFRACTION5chain 'A' and (resid 177 through 212 )
6X-RAY DIFFRACTION6chain 'A' and (resid 213 through 265 )
7X-RAY DIFFRACTION7chain 'A' and (resid 266 through 279 )

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