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- PDB-3sig: The X-ray crystal structure of poly(ADP-ribose) glycohydrolase (P... -

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Basic information

Entry
Database: PDB / ID: 3sig
TitleThe X-ray crystal structure of poly(ADP-ribose) glycohydrolase (PARG) bound to ADP-ribose from Thermomonospora curvata
Componentspoly(ADP-ribose) glycohydrolase
KeywordsHYDROLASE / poly ADP ribose
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 speciesThermomonospora curvata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsLeys, D. / Dunstan, M.S.
CitationJournal: Nature / Year: 2011
Title: The structure and catalytic mechanism of a poly(ADP-ribose) glycohydrolase.
Authors: Slade, D. / Dunstan, M.S. / Barkauskaite, E. / Weston, R. / Lafite, P. / Dixon, N. / Ahel, M. / Leys, D. / Ahel, I.
History
DepositionJun 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Database references
Revision 1.2Oct 12, 2011Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3232
Polymers29,7641
Non-polymers5591
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.130, 106.390, 44.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein poly(ADP-ribose) glycohydrolase / PARG


Mass: 29763.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermomonospora curvata (bacteria) / Strain: ATCC 19995 / DSM 43183 / JCM 3096 / NCIMB 10081 / Gene: Tcur_1721 / Production host: Escherichia coli (E. coli)
References: UniProt: D1AC29, poly(ADP-ribose) glycohydrolase
#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.: 348 / 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: 1.98 Å3/Da / Density % sol: 37.82 %
Crystal growMethod: sitting drop, vapor diffusion / pH: 9
Details: 10% PEG6000, 0.1 M Bicine, pH 9.0, SITTING DROP, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.976
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.28→23.5 Å / Num. all: 66929 / Num. obs: 66929 / % possible obs: 100 %

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
SOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SIH

3sih


Resolution: 1.28→23.495 Å / Occupancy max: 1 / Occupancy min: 0.41 / FOM work R set: 0.9169 / SU ML: 0.12 / σ(F): 1.37 / Phase error: 14.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1608 2981 5.05 %
Rwork0.1492 --
obs0.1498 59037 88.2 %
all-66929 -
Solvent computationShrinkage radii: 0.41 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.411 Å2 / ksol: 0.452 e/Å3
Displacement parametersBiso max: 103.25 Å2 / Biso mean: 19.3074 Å2 / Biso min: 5.19 Å2
Baniso -1Baniso -2Baniso -3
1--0.0641 Å20 Å2-0 Å2
2--0.1326 Å20 Å2
3----0.0685 Å2
Refine analyzeLuzzati sigma a obs: 0.12 Å
Refinement stepCycle: LAST / Resolution: 1.28→23.495 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2028 0 36 348 2412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122138
X-RAY DIFFRACTIONf_angle_d1.5182911
X-RAY DIFFRACTIONf_chiral_restr0.093314
X-RAY DIFFRACTIONf_plane_restr0.008385
X-RAY DIFFRACTIONf_dihedral_angle_d19.796807
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.28-1.3010.25671300.25462424255488
1.301-1.32340.2071390.21442587272694
1.3234-1.34750.21681350.20072557269294
1.3475-1.37340.20331440.19282596274094
1.3734-1.40140.22451640.17972596276095
1.4014-1.43190.19441570.17252587274494
1.4319-1.46520.17111200.16692624274495
1.4652-1.50180.1851400.15642634277495
1.5018-1.54240.18731360.14972636277295
1.5424-1.58780.16421190.1482689280896
1.5878-1.6390.1741380.14012659279796
1.639-1.69760.16551460.14032667281396
1.6976-1.76560.15211280.13672687281596
1.7656-1.84590.15831380.13922712285097
1.8459-1.94320.15241490.1422696284598
1.9432-2.06480.19261510.13972733288498
2.0648-2.22410.13961520.13492721287397
2.2241-2.44780.14761550.13232736289198
2.4478-2.80150.17021370.14792817295498
2.8015-3.52760.14011420.14382834297699
3.5276-23.49920.14131610.15052864302596
Refinement TLS params.Method: refined / Origin x: 4.9168 Å / Origin y: -13.9176 Å / Origin z: -13.2817 Å
111213212223313233
T0.0504 Å2-0.0025 Å20.0019 Å2-0.0558 Å20.003 Å2--0.0417 Å2
L1.2404 °2-0.6272 °20.3417 °2-1.0916 °2-0.142 °2--0.5759 °2
S0.0438 Å °0.0481 Å °0.0341 Å °-0.0172 Å °-0.0487 Å °-0.0052 Å °-0.0247 Å °0.0608 Å °0.0036 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 280
2X-RAY DIFFRACTION1allA1 - 348

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