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- PDB-4epq: canonical poly(ADP-ribose) glycohydrolase RBPI inhibitor complex ... -

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Basic information

Entry
Database: PDB / ID: 4epq
Titlecanonical poly(ADP-ribose) glycohydrolase RBPI inhibitor complex from Tetrahymena thermophila
ComponentsPoly(ADP-ribose) glycohydrolase
KeywordsHYDROLASE/INHIBITOR / Macro domain / PAR / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


poly(ADP-ribose) glycohydrolase / poly(ADP-ribose) glycohydrolase activity / regulation of DNA repair / carbohydrate metabolic process
Similarity search - Function
: / Poly (ADP-ribose) glycohydrolase (PARG), helical domain / Poly (ADP-ribose) glycohydrolase (PARG), catalytic domain / Poly(ADP-ribose) glycohydrolase / Poly (ADP-ribose) glycohydrolase (PARG), Macro domain fold
Similarity search - Domain/homology
Chem-0RR / poly(ADP-ribose) glycohydrolase
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.399 Å
AuthorsDunstan, M.S. / Leys, D.
CitationJournal: Nat Commun / Year: 2012
Title: Structure and mechanism of a canonical poly(ADP-ribose) glycohydrolase.
Authors: Dunstan, M.S. / Barkauskaite, E. / Lafite, P. / Knezevic, C.E. / Brassington, A. / Ahel, M. / Hergenrother, P.J. / Leys, D. / Ahel, I.
History
DepositionApr 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,4012
Polymers55,8731
Non-polymers5281
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.680, 80.680, 89.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Poly(ADP-ribose) glycohydrolase


Mass: 55873.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila (eukaryote) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: I6L8L8*PLUS
#2: Chemical ChemComp-0RR / 3-{(5Z)-5-[5-chloro-1-(2,6-dichlorobenzyl)-2-oxo-1,2-dihydro-3H-indol-3-ylidene]-4-oxo-2-thioxo-1,3-thiazolidin-3-yl}propanoic acid


Mass: 527.828 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H13Cl3N2O4S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.6 Å3/Da / Density % sol: 52.77 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.399→36.771 Å / Num. obs: 22497

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7_650) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EPP

4epp


Resolution: 2.399→36.771 Å / SU ML: 0.29 / σ(F): 2 / Phase error: 23.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2307 1151 5.12 %
Rwork0.165 --
obs0.1683 22497 99.88 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.925 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.203 Å2-0 Å20 Å2
2---0.203 Å2-0 Å2
3---0.406 Å2
Refinement stepCycle: LAST / Resolution: 2.399→36.771 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3617 0 32 69 3718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083714
X-RAY DIFFRACTIONf_angle_d1.1514987
X-RAY DIFFRACTIONf_dihedral_angle_d16.6471428
X-RAY DIFFRACTIONf_chiral_restr0.075535
X-RAY DIFFRACTIONf_plane_restr0.004635
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.399-2.50780.34871670.26782634X-RAY DIFFRACTION99
2.5078-2.640.2791460.23472631X-RAY DIFFRACTION100
2.64-2.80540.2781430.20192668X-RAY DIFFRACTION100
2.8054-3.02190.28231440.19952668X-RAY DIFFRACTION100
3.0219-3.32580.25191420.18112643X-RAY DIFFRACTION100
3.3258-3.80660.23511590.16522672X-RAY DIFFRACTION100
3.8066-4.79430.17611260.12632703X-RAY DIFFRACTION100
4.7943-36.7710.20051240.14522727X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 4.9511 Å / Origin y: 20.9225 Å / Origin z: -1.0772 Å
111213212223313233
T0.3492 Å20.007 Å20.0115 Å2-0.119 Å2-0.0004 Å2--0.1993 Å2
L0.7757 °2-0.114 °20.4394 °2-1.1361 °20.4281 °2--1.7716 °2
S0.0145 Å °-0.0409 Å °0.0972 Å °-0.1855 Å °0.0789 Å °-0.0249 Å °-0.555 Å °0.1055 Å °0.072 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 14:452 OR RESID 501:501 OR RESID 601:669 ) )A14 - 452
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 14:452 OR RESID 501:501 OR RESID 601:669 ) )A501
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 14:452 OR RESID 501:501 OR RESID 601:669 ) )A601 - 669

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