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- PDB-3sij: The X-ray crystal structure of poly(ADP-ribose) glycohydrolase E1... -

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Basic information

Entry
Database: PDB / ID: 3sij
TitleThe X-ray crystal structure of poly(ADP-ribose) glycohydrolase E115A mutant from Thermomonospora curvata
Componentspoly(ADP-ribose) glycohydrolase
KeywordsHYDROLASE
Function / homologyConserved 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 / Microbial-type PARG catalytic domain-containing protein
Function and homology information
Biological speciesThermomonospora curvata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDunstan, M.S. / Leys, D.
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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: poly(ADP-ribose) glycohydrolase


Theoretical massNumber of molelcules
Total (without water)29,7061
Polymers29,7061
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.100, 105.430, 44.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 29705.648 Da / Num. of mol.: 1 / Mutation: E115A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 1.97 Å3/Da / Density % sol: 37.43 %
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: 1.9→45.251 Å / Num. all: 18831 / Num. obs: 18831 / % possible obs: 100 %

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Processing

Software
NameVersionClassificationNB
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SIG

3sig


Resolution: 1.9→45.251 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8645 / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 20.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 975 5.18 %RANDOM
Rwork0.1771 ---
obs0.1794 18831 98.4 %-
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.237 Å2 / ksol: 0.367 e/Å3
Displacement parametersBiso max: 113.96 Å2 / Biso mean: 33.3747 Å2 / Biso min: 10.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.2951 Å20 Å2-0 Å2
2--1.3368 Å20 Å2
3----1.0417 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.251 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2024 0 0 123 2147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072073
X-RAY DIFFRACTIONf_angle_d1.0152813
X-RAY DIFFRACTIONf_chiral_restr0.069303
X-RAY DIFFRACTIONf_plane_restr0.004377
X-RAY DIFFRACTIONf_dihedral_angle_d13.039744
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-2.00020.29691440.22212467261197
2.0002-2.12550.25261290.18962478260798
2.1255-2.28960.23631360.18152546268299
2.2896-2.520.26931390.18152499263898
2.52-2.88460.25931520.192531268399
2.8846-3.63410.21831430.17292601274499
3.6341-45.26360.18681320.1642731286399
Refinement TLS params.Method: refined / Origin x: 4.8747 Å / Origin y: -13.863 Å / Origin z: -13.2311 Å
111213212223313233
T0.1449 Å2-0.035 Å2-0.0041 Å2-0.1446 Å20.0278 Å2--0.1174 Å2
L0.6512 °2-0.7923 °20.4595 °2-1.0635 °2-0.1204 °2--1.1406 °2
S0.0539 Å °0.1312 Å °-0.0053 Å °-0.0384 Å °-0.1115 Å °0.032 Å °-0.2542 Å °0.2816 Å °0.0284 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 276
2X-RAY DIFFRACTION1allA1 - 402

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