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- PDB-4epp: Canonical poly(ADP-ribose) glycohydrolase from Tetrahymena thermo... -

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Basic information

Entry
Database: PDB / ID: 4epp
TitleCanonical poly(ADP-ribose) glycohydrolase from Tetrahymena thermophila.
ComponentsPoly(ADP-ribose) glycohydrolase
KeywordsHYDROLASE / Marco domain / PAR
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
ADENOSINE-5-DIPHOSPHORIBOSE / poly(ADP-ribose) glycohydrolase
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 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 20, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)112,8914
Polymers111,7722
Non-polymers1,1192
Water18,0151000
1
A: Poly(ADP-ribose) glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4452
Polymers55,8861
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Poly(ADP-ribose) glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4452
Polymers55,8861
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)112.700, 112.700, 88.600
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: 55886.027 Da / Num. of mol.: 2
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-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1000 / 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: 2.52 Å3/Da / Density % sol: 51.13 %

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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: 1.95→19.923 Å / Num. obs: 80676

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SOLVEphasing
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
XDSdata reduction
XDSdata scaling
PHENIX1.7_650refinement
RefinementMethod to determine structure: SAD / Resolution: 1.95→19.923 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8812 / SU ML: 0.21 / σ(F): 1.99 / Phase error: 19.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2069 4023 4.99 %
Rwork0.167 76653 -
obs0.169 80676 99.98 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.12 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso max: 77.25 Å2 / Biso mean: 28.6497 Å2 / Biso min: 10.57 Å2
Baniso -1Baniso -2Baniso -3
1-1.0787 Å20 Å2-0 Å2
2--1.0787 Å20 Å2
3----2.1574 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7236 0 72 1000 8308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077438
X-RAY DIFFRACTIONf_angle_d1.0399992
X-RAY DIFFRACTIONf_chiral_restr0.0721084
X-RAY DIFFRACTIONf_plane_restr0.0031266
X-RAY DIFFRACTIONf_dihedral_angle_d17.7872942
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.95-1.97290.25761200.252626402760
1.9729-1.9970.27861280.235626552783
1.997-2.02220.28581440.214526462790
2.0222-2.04880.26591420.211826262768
2.0488-2.07680.24751170.198326292746
2.0768-2.10650.23771320.192426492781
2.1065-2.13790.24551370.191726412778
2.1379-2.17130.25151330.177626442777
2.1713-2.20680.21141440.173826392783
2.2068-2.24480.20711280.170426202748
2.2448-2.28560.19781290.172526342763
2.2856-2.32950.22831280.170126232751
2.3295-2.37690.22421260.164126642790
2.3769-2.42850.22271360.168126492785
2.4285-2.48490.21411330.169626122745
2.4849-2.5470.24581520.172826402792
2.547-2.61570.2131660.175826302796
2.6157-2.69250.22291430.16226292772
2.6925-2.77920.21031380.171626032741
2.7792-2.87820.18761400.163126702810
2.8782-2.99310.20821460.164626442790
2.9931-3.12880.19981270.163126642791
3.1288-3.29310.21241490.163326162765
3.2931-3.49840.18411390.15526782817
3.4984-3.76680.20621340.1526502784
3.7668-4.14280.17241540.140726212775
4.1428-4.73520.18381530.136526622815
4.7352-5.93950.18471440.175926892833
5.9395-19.9230.19871610.174626862847

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