[English] 日本語
Yorodumi
- PDB-7kg1: Structure of human PARG complexed with PARG-002 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kg1
TitleStructure of human PARG complexed with PARG-002
ComponentsPoly(ADP-ribose) glycohydrolase
KeywordsHYDROLASE/HYDROLASE inhibitor / HYDROLASE / hydrolase inhibitor complex / methyl xanthine / HYDROLASE-HYDROLASE inhibitor complex
Function / homology
Function and homology information


nucleotide-sugar metabolic process / poly(ADP-ribose) glycohydrolase / poly(ADP-ribose) glycohydrolase activity / ATP generation from poly-ADP-D-ribose / POLB-Dependent Long Patch Base Excision Repair / regulation of DNA repair / base-excision repair, gap-filling / carbohydrate metabolic process / nuclear body / mitochondrial matrix ...nucleotide-sugar metabolic process / poly(ADP-ribose) glycohydrolase / poly(ADP-ribose) glycohydrolase activity / ATP generation from poly-ADP-D-ribose / POLB-Dependent Long Patch Base Excision Repair / regulation of DNA repair / base-excision repair, gap-filling / carbohydrate metabolic process / nuclear body / mitochondrial matrix / nucleoplasm / nucleus / cytosol / 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
CACODYLATE ION / Chem-WDD / Poly(ADP-ribose) glycohydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBrosey, C.A. / Balapiti-Modarage, L.P.F. / Warden, L.S. / Jones, D.E. / Ahmed, Z. / Tainer, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA200231 United States
CitationJournal: Prog.Biophys.Mol.Biol. / Year: 2021
Title: Targeting SARS-CoV-2 Nsp3 macrodomain structure with insights from human poly(ADP-ribose) glycohydrolase (PARG) structures with inhibitors.
Authors: Brosey, C.A. / Houl, J.H. / Katsonis, P. / Balapiti-Modarage, L.P.F. / Bommagani, S. / Arvai, A. / Moiani, D. / Bacolla, A. / Link, T. / Warden, L.S. / Lichtarge, O. / Jones, D.E. / Ahmed, Z. / Tainer, J.A.
History
DepositionOct 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)62,44314
Polymers61,0201
Non-polymers1,42213
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.463, 88.964, 95.049
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Poly(ADP-ribose) glycohydrolase


Mass: 61020.375 Da / Num. of mol.: 1 / Mutation: K616A, Q617A, K618A, E688A, K689A, K690A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARG / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2
References: UniProt: Q86W56, poly(ADP-ribose) glycohydrolase

-
Non-polymers , 6 types, 316 molecules

#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-WDD / 1,3-dimethyl-8-{[2-(morpholin-4-yl)ethyl]amino}-3,7-dihydro-1H-purine-2,6-dione


Mass: 308.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H20N6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M PCTP, pH 7.5, 0.2 M AmSO4, 18-23% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2020
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.65→38.66 Å / Num. obs: 68294 / % possible obs: 99.74 % / Redundancy: 13.1 % / Biso Wilson estimate: 26.99 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.05614 / Rpim(I) all: 0.01608 / Rrim(I) all: 0.05845 / Net I/σ(I): 24.76
Reflection shellResolution: 1.65→1.709 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.655 / Mean I/σ(I) obs: 1.74 / Num. unique obs: 6747 / CC1/2: 0.745 / CC star: 0.924 / Rpim(I) all: 0.4605 / Rrim(I) all: 1.719 / % possible all: 99.69

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B1G

4b1g


Resolution: 1.65→38.66 Å / SU ML: 0.1482 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.981
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1981 3407 4.99 %
Rwork0.1741 64868 -
obs0.1753 68275 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.24 Å2
Refinement stepCycle: LAST / Resolution: 1.65→38.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3876 0 80 303 4259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01384087
X-RAY DIFFRACTIONf_angle_d1.10865566
X-RAY DIFFRACTIONf_chiral_restr0.0724612
X-RAY DIFFRACTIONf_plane_restr0.0087707
X-RAY DIFFRACTIONf_dihedral_angle_d14.29361440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.33761360.27082668X-RAY DIFFRACTION99.75
1.67-1.70.28921500.25922662X-RAY DIFFRACTION99.68
1.7-1.730.25831210.24282672X-RAY DIFFRACTION99.61
1.73-1.750.25591610.22862669X-RAY DIFFRACTION99.86
1.75-1.780.2671400.22062675X-RAY DIFFRACTION99.75
1.78-1.820.24991440.21742654X-RAY DIFFRACTION99.4
1.82-1.850.23851390.19192692X-RAY DIFFRACTION99.86
1.85-1.890.2321400.18132644X-RAY DIFFRACTION99.86
1.89-1.930.21311330.17272680X-RAY DIFFRACTION99.79
1.93-1.970.20871290.16852717X-RAY DIFFRACTION99.82
1.97-2.020.21281330.15922697X-RAY DIFFRACTION99.93
2.02-2.080.18251420.15992668X-RAY DIFFRACTION99.89
2.08-2.140.161270.15012712X-RAY DIFFRACTION99.72
2.14-2.210.17411450.15542670X-RAY DIFFRACTION99.29
2.21-2.290.16811300.15092706X-RAY DIFFRACTION99.86
2.29-2.380.20811460.16092683X-RAY DIFFRACTION99.86
2.38-2.490.19391270.16072720X-RAY DIFFRACTION99.72
2.49-2.620.20271380.16552721X-RAY DIFFRACTION99.9
2.62-2.780.20131790.16392668X-RAY DIFFRACTION99.65
2.78-30.17781460.17282713X-RAY DIFFRACTION99.58
3-3.30.2331430.17432740X-RAY DIFFRACTION99.93
3.3-3.780.17731680.16482732X-RAY DIFFRACTION100
3.78-4.760.16581370.15432798X-RAY DIFFRACTION99.73
4.76-38.660.21341530.20892907X-RAY DIFFRACTION99.71
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)
13.436145356073.133373785422.308357978513.693923635562.978864320173.888424115040.0644353228519-0.1444184121420.530365631425-0.193046514807-0.05459072582050.63096599755-0.207754113862-0.374771106574-0.01797542383590.3055279092480.0177760480011-0.03031257454320.2355188936770.09198702235560.458719872378.8561364713112.6523225474-4.17374614202
22.48500013883-0.3307537895430.6343591067661.39019497355-0.5021468680160.72101450061-0.04034417123630.15766368545-0.422699032609-0.1467335186720.1361473593880.1251186255110.08791300798670.0439419804183-0.1010620291540.226653185605-0.02419311875690.01301279658360.219637868217-0.04389554913120.28251158489110.2321017268-23.2635597228-7.62632415539
31.440755193220.862947936627-0.03168537529842.05581194863-0.04631663553480.126041830634-0.1050747409630.269044330537-0.0233522219074-0.2579937596140.1439407011080.0087741501885-0.04696843147970.0191219467704-0.04448339241710.241275742371-0.02204029245220.002749573627270.261554590247-0.006518974410630.18266113230314.7724803697-8.00680081854-10.163915533
42.454073768211.15646805596-0.1011250598032.58792567563-0.4223596507950.400944295339-0.0726106868880.06441700501540.001400873691-0.06160740269550.100023477348-0.0613330451369-0.08723085031630.0396853641145-0.02526216493320.227900963802-0.0122665030588-0.0008834274131290.220684161643-0.01509021784880.17782741727318.4324292964-1.34584357876-5.79298246875
53.475110539291.4489508306-0.7222504389322.89630165461-0.7270581158492.08319099401-0.06134176530220.2537801576770.412230309888-0.160521002870.105487812621-0.068879664498-0.07985365864960.051636335814-0.03759224947190.262893599563-0.0243801843143-0.001963775389680.2126021057450.03812207043910.2624344366829.318601975117.0493421253-10.2394378329
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 451 through 479 )451 - 4791 - 29
22chain 'A' and (resid 480 through 601 )480 - 60130 - 140
33chain 'A' and (resid 602 through 725 )602 - 725141 - 265
44chain 'A' and (resid 726 through 837 )726 - 837266 - 377
55chain 'A' and (resid 838 through 962 )838 - 962378 - 505

+
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