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

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Basic information

Entry
Database: PDB / ID: 3sih
TitleThe X-ray crystal structure of poly(ADP-ribose) glycohydrolase (PARG) from Thermomonospora curvata
Componentspoly(ADP-ribose) glycohydrolase
KeywordsHYDROLASE / poly ADP-ribose
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 / SAD / Resolution: 1.5 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 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)29,7641
Polymers29,7641
Non-polymers00
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.245, 50.074, 105.517
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: 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 1.96 Å3/Da / Density % sol: 37.36 %
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 315 / Detector: CCD / Date: Feb 24, 2011
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.5→40.803 Å / Num. all: 38375 / Num. obs: 37023 / % possible obs: 96.5 %

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Processing

Software
NameVersionClassificationNB
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→33.156 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.853 / SU ML: 0.16 / σ(F): 2 / Phase error: 21.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.214 1848 4.99 %
Rwork0.1843 --
obs0.1858 37023 96.48 %
all-38375 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.031 Å2 / ksol: 0.357 e/Å3
Displacement parametersBiso max: 113.54 Å2 / Biso mean: 28.2533 Å2 / Biso min: 7.62 Å2
Baniso -1Baniso -2Baniso -3
1--4.9998 Å2-0 Å20 Å2
2---3.4908 Å2-0 Å2
3---8.4906 Å2
Refine analyzeLuzzati sigma a obs: 0.16 Å
Refinement stepCycle: LAST / Resolution: 1.5→33.156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2080 0 0 226 2306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062131
X-RAY DIFFRACTIONf_angle_d1.0062894
X-RAY DIFFRACTIONf_chiral_restr0.075311
X-RAY DIFFRACTIONf_plane_restr0.004390
X-RAY DIFFRACTIONf_dihedral_angle_d15.535758
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5001-1.54070.25751350.24062701283697
1.5407-1.5860.24111530.22452712286598
1.586-1.63720.27451500.21942718286899
1.6372-1.69570.28041160.21282740285699
1.6957-1.76360.22381380.1982742288098
1.7636-1.84380.24221250.18322739286498
1.8438-1.9410.2311360.19062693282998
1.941-2.06260.21781410.18562699284097
2.0626-2.22190.1961560.17292729288597
2.2219-2.44540.23821370.17892688282596
2.4454-2.79910.22181620.18612684284695
2.7991-3.52590.17711450.17662657280294
3.5259-33.16430.19391540.16692662281689
Refinement TLS params.Method: refined / Origin x: 35.1075 Å / Origin y: 29.5077 Å / Origin z: 13.8455 Å
111213212223313233
T0.0572 Å2-0.0069 Å20.0135 Å2-0.0762 Å20.0295 Å2--0.0724 Å2
L1.6512 °2-0.8735 °2-0.4205 °2-2.0605 °21.4449 °2--1.7502 °2
S0.0663 Å °0.1918 Å °0.2877 Å °-0.0637 Å °0.0499 Å °-0.1391 Å °-0.0035 Å °0.0393 Å °-0.1035 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 276
2X-RAY DIFFRACTION1allA1 - 505

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