[English] 日本語
Yorodumi
- PDB-8adk: Poly(ADP-ribose) glycohydrolase (PARG) from Drosophila melanogaster -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8adk
TitlePoly(ADP-ribose) glycohydrolase (PARG) from Drosophila melanogaster
ComponentsPoly(ADP-ribose) glycohydrolase
KeywordsHYDROLASE / PARG / POLY(ADP-RIBOSE) GLYCOHYDROLASE / ADP-RIBOSE
Function / homology
Function and homology information


POLB-Dependent Long Patch Base Excision Repair / female germ-line stem cell population maintenance / ADP-ribosylserine hydrolase activity / nucleotide-sugar metabolic process / Cajal body organization / poly(ADP-ribose) glycohydrolase activity / poly(ADP-ribose) glycohydrolase / ATP generation from poly-ADP-D-ribose / maintenance of protein location in nucleus / regulation of RNA splicing ...POLB-Dependent Long Patch Base Excision Repair / female germ-line stem cell population maintenance / ADP-ribosylserine hydrolase activity / nucleotide-sugar metabolic process / Cajal body organization / poly(ADP-ribose) glycohydrolase activity / poly(ADP-ribose) glycohydrolase / ATP generation from poly-ADP-D-ribose / maintenance of protein location in nucleus / regulation of RNA splicing / site of DNA damage / regulation of DNA repair / heterochromatin formation / response to heat / carbohydrate metabolic process / DNA damage response / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Poly(ADP-ribose) glycohydrolase / Poly (ADP-ribose) glycohydrolase (PARG), catalytic domain / : / Poly (ADP-ribose) glycohydrolase (PARG), Macro domain fold / Poly (ADP-ribose) glycohydrolase (PARG), helical domain
Similarity search - Domain/homology
Poly(ADP-ribose) glycohydrolase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.474 Å
AuthorsAriza, A. / Fontana, P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust210634 United Kingdom
CitationJournal: Nat Commun / Year: 2023
Title: Serine ADP-ribosylation in Drosophila provides insights into the evolution of reversible ADP-ribosylation signalling.
Authors: Fontana, P. / Buch-Larsen, S.C. / Suyari, O. / Smith, R. / Suskiewicz, M.J. / Schutzenhofer, K. / Ariza, A. / Rack, J.G.M. / Nielsen, M.L. / Ahel, I.
History
DepositionJul 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Poly(ADP-ribose) glycohydrolase
B: Poly(ADP-ribose) glycohydrolase
C: Poly(ADP-ribose) glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,21218
Polymers197,9813
Non-polymers1,23115
Water4,990277
1
A: Poly(ADP-ribose) glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5338
Polymers65,9941
Non-polymers5397
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly(ADP-ribose) glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3095
Polymers65,9941
Non-polymers3164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Poly(ADP-ribose) glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3705
Polymers65,9941
Non-polymers3764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.433, 115.622, 122.913
Angle α, β, γ (deg.)90.000, 112.214, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A
53A
63A

NCS domain segments:

Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LYS / End label comp-ID: LYS / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 26 - 549 / Label seq-ID: 46 - 569

Dom-IDComponent-IDEns-ID
111
211
322
422
533
633

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6

-
Components

#1: Protein Poly(ADP-ribose) glycohydrolase


Mass: 65993.641 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Parg, CG2864 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
References: UniProt: O46043, poly(ADP-ribose) glycohydrolase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.48 Å3/Da / Density % sol: 64.65 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 19% (v/v) PEG3350, 210 mM Na2SO4, 100 mM BisTris propane pH 7.2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97958 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.458→59.025 Å / Num. obs: 88137 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.046 / Net I/σ(I): 9.7
Reflection shellResolution: 2.46→2.52 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.618 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 6515 / CC1/2: 0.579 / Rpim(I) all: 0.673 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6hmk

6hmk


Resolution: 2.474→59.025 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.223 / WRfactor Rwork: 0.167 / SU B: 19.834 / SU ML: 0.204 / Average fsc free: 0.9554 / Average fsc work: 0.9702 / Cross valid method: FREE R-VALUE / ESU R: 0.294 / ESU R Free: 0.229
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2277 4166 4.86 %
Rwork0.1771 81549 -
all0.18 --
obs-85715 99.239 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 66.609 Å2
Baniso -1Baniso -2Baniso -3
1--1.529 Å2-0 Å2-1.236 Å2
2--3.181 Å2-0 Å2
3----0.482 Å2
Refinement stepCycle: LAST / Resolution: 2.474→59.025 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12552 0 70 277 12899
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01212964
X-RAY DIFFRACTIONr_bond_other_d0.0120.01611638
X-RAY DIFFRACTIONr_angle_refined_deg1.8951.64417573
X-RAY DIFFRACTIONr_angle_other_deg0.6531.5527175
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.81351551
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.11510117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.051102184
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.64710642
X-RAY DIFFRACTIONr_chiral_restr0.0840.21875
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214814
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022683
X-RAY DIFFRACTIONr_nbd_refined0.2130.22411
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.211026
X-RAY DIFFRACTIONr_nbtor_refined0.1780.25988
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.26683
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2317
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2570.28
X-RAY DIFFRACTIONr_nbd_other0.1920.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1810.22
X-RAY DIFFRACTIONr_mcbond_it7.0525.5676204
X-RAY DIFFRACTIONr_mcbond_other7.0475.5676204
X-RAY DIFFRACTIONr_mcangle_it9.4748.3217746
X-RAY DIFFRACTIONr_mcangle_other9.4768.3227747
X-RAY DIFFRACTIONr_scbond_it8.266.0076760
X-RAY DIFFRACTIONr_scbond_other7.5655.9996741
X-RAY DIFFRACTIONr_scangle_it10.2888.799824
X-RAY DIFFRACTIONr_scangle_other10.0628.7859795
X-RAY DIFFRACTIONr_lrange_it11.86465.59613827
X-RAY DIFFRACTIONr_lrange_other11.86765.58713806
X-RAY DIFFRACTIONr_ncsr_local_group_10.0730.0517538
X-RAY DIFFRACTIONr_ncsr_local_group_20.0660.0517626
X-RAY DIFFRACTIONr_ncsr_local_group_30.0740.0517477
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.073450.05008
12AX-RAY DIFFRACTIONLocal ncs0.073450.05008
23AX-RAY DIFFRACTIONLocal ncs0.066360.05009
24AX-RAY DIFFRACTIONLocal ncs0.066360.05009
35AX-RAY DIFFRACTIONLocal ncs0.074210.05008
36AX-RAY DIFFRACTIONLocal ncs0.074210.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.474-2.5380.3332580.31656600.31763020.9310.92993.90670.318
2.538-2.6080.3463330.30158970.30462440.9230.94199.77580.302
2.608-2.6830.3193380.2956620.29260230.9330.94899.61810.286
2.683-2.7660.3312690.27455410.27758320.9320.95799.62280.266
2.766-2.8560.2872810.23953940.24156990.9460.96599.57890.227
2.856-2.9560.2932590.20351740.20754500.9480.97499.68810.189
2.956-3.0670.2482350.19650550.19853060.9560.97699.69850.181
3.067-3.1920.2492810.19848000.20151000.9580.97699.62750.184
3.192-3.3340.2522290.19146380.19349060.9630.9899.20510.18
3.334-3.4960.2392030.19544330.19746660.9670.9899.3570.185
3.496-3.6840.2312210.18442280.18644590.9710.98499.77570.176
3.684-3.9070.2162260.17540240.17742500.9740.9841000.167
3.907-4.1750.1782050.14937140.1539210.9810.98799.9490.144
4.175-4.5080.1761850.12535430.12837290.9820.9999.97320.123
4.508-4.9350.191480.13632690.13934190.980.98999.94150.135
4.935-5.5130.2141260.14729580.1530920.9750.98899.74130.146
5.513-6.3570.2241370.1525880.15427270.9750.98799.92670.149
6.357-7.7630.166970.14622410.14723390.9840.98799.95720.148
7.763-10.8850.154810.11217290.11418150.9870.99299.72450.119
10.885-59.0250.302540.22310010.22710640.9350.96599.15410.267
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)
10.62550.14160.12330.45-0.36730.5151-0.1066-0.0120.0479-0.09110.0031-0.0476-0.0668-0.01920.10350.15390.0622-0.01390.08750.0260.0343.011546.127-45.121
20.83510.10260.62810.35570.50141.03620.04810.0008-0.08520.03870.1324-0.13380.0360.0944-0.18060.06290.0662-0.06880.1292-0.08580.102634.275634.203-5.809
30.74190.02360.15651.1678-0.39610.23460.0971-0.08510.0584-0.2003-0.1557-0.03620.13440.02490.05860.1220.05940.00810.0922-0.03710.0343-25.9075.1871-31.5616
Refinement TLS groupSelection: ALL

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more