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- PDB-3uek: Crystal structure of the catalytic domain of rat poly (ADP-ribose... -

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Basic information

Entry
Database: PDB / ID: 3uek
TitleCrystal structure of the catalytic domain of rat poly (ADP-ribose) glycohydrolase
ComponentsPoly(ADP-ribose) glycohydrolase
KeywordsHYDROLASE / mammalian PARG / macrodomain
Function / homology
Function and homology information


POLB-Dependent Long Patch Base Excision Repair / nucleotide-sugar metabolic process / poly(ADP-ribose) glycohydrolase activity / poly(ADP-ribose) glycohydrolase / ATP generation from poly-ADP-D-ribose / detection of bacterium / regulation of DNA repair / positive regulation of DNA repair / carbohydrate metabolic process / DNA damage response ...POLB-Dependent Long Patch Base Excision Repair / nucleotide-sugar metabolic process / poly(ADP-ribose) glycohydrolase activity / poly(ADP-ribose) glycohydrolase / ATP generation from poly-ADP-D-ribose / detection of bacterium / regulation of DNA repair / positive regulation of DNA repair / carbohydrate metabolic process / DNA damage response / chromatin binding / chromatin / nucleus / cytoplasm / cytosol
Similarity search - Function
Poly(ADP-ribose) glycohydrolase / Poly (ADP-ribose) glycohydrolase (PARG), catalytic domain / : / Poly (ADP-ribose) glycohydrolase (PARG), Macro domain fold / Poly (ADP-ribose) glycohydrolase (PARG), helical domain
Similarity search - Domain/homology
Poly(ADP-ribose) glycohydrolase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsKim, I.K. / Kiefer, J.R. / Stegemann, R.A. / Classen, S. / Tainer, J.A. / Ellenberger, T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Structure of mammalian poly(ADP-ribose) glycohydrolase reveals a flexible tyrosine clasp as a substrate-binding element.
Authors: Kim, I.K. / Kiefer, J.R. / Ho, C.M. / Stegeman, R.A. / Classen, S. / Tainer, J.A. / Ellenberger, T.
History
DepositionOct 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2012Group: Database references
Revision 1.2Feb 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)67,7801
Polymers67,7801
Non-polymers00
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)126.537, 199.497, 50.511
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Poly(ADP-ribose) glycohydrolase


Mass: 67780.156 Da / Num. of mol.: 1 / Fragment: UNP residues 385-972
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Parg / Production host: Escherichia coli (E. coli)
References: UniProt: Q9QYM2, poly(ADP-ribose) glycohydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.35 Å3/Da / Density % sol: 47.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 16-20% PEG2000 monomethylether, 0.1M Tris-HCl pH7.5, 0.1M NaCl, 0.2M potassium thiocyanate., VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.12712 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 8, 2011
RadiationMonochromator: Cryo-cooled Si(111) double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12712 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 43903 / % possible obs: 98.1 %
Reflection shellResolution: 1.95→2 Å / % possible all: 85.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 9.187 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21659 2343 5.1 %RANDOM
Rwork0.1805 ---
obs0.18232 43903 98.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.149 Å2
Baniso -1Baniso -2Baniso -3
1-1.97 Å20 Å20 Å2
2---3.03 Å20 Å2
3---1.07 Å2
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4151 0 0 203 4354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.024260
X-RAY DIFFRACTIONr_bond_other_d0.0010.022935
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.9625789
X-RAY DIFFRACTIONr_angle_other_deg0.98637112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2115520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.80123.3200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.79115700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3791533
X-RAY DIFFRACTIONr_chiral_restr0.1050.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214752
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02913
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 155 -
Rwork0.325 2598 -
obs--85.36 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5508-0.0495-0.18473.27060.58090.7098-0.04810.0244-0.12660.0649-0.02740.0359-0.02040.07470.07550.02640.02460.02160.0860.02410.0399-43.6159-32.3665.2803
20.53980.29680.03842.51770.44690.6491-0.00680.001-0.070.0263-0.04730.0899-0.07770.04060.05410.04050.02380.02390.11680.02860.0434-46.4766-29.975.3097
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A438 - 958
2X-RAY DIFFRACTION2A1 - 179

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