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

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Basic information

Entry
Database: PDB / ID: 3uel
TitleCrystal structure of the catalytic domain of rat poly (ADP-ribose) glycohydrolase bound to ADP-HPD
ComponentsPoly(ADP-ribose) glycohydrolase
KeywordsHYDROLASE / mammalian PARG / macrodomain / ADP-HPD
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
Chem-A1R / Poly(ADP-ribose) glycohydrolase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 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 / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)204,9676
Polymers203,3403
Non-polymers1,6273
Water00
1
A: Poly(ADP-ribose) glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3222
Polymers67,7801
Non-polymers5421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Poly(ADP-ribose) glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3222
Polymers67,7801
Non-polymers5421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Poly(ADP-ribose) glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3222
Polymers67,7801
Non-polymers5421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)130.773, 195.989, 163.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.988584, 0.039094, -0.145508), (0.054861, 0.992854, -0.105978), (0.140325, -0.112751, -0.983665)136.62363, -3.28051, 16.33627
3given(-0.994212, -0.053887, -0.092947), (0.047685, -0.996565, 0.067701), (-0.096276, 0.062876, 0.993367)135.74771, -4.44907, -19.35456

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Components

#1: Protein Poly(ADP-ribose) glycohydrolase


Mass: 67780.156 Da / Num. of mol.: 3 / 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: Chemical ChemComp-A1R / 5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE


Mass: 542.332 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H24N6O12P2

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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: 2.58 Å3/Da / Density % sol: 52.24 %
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. 200 uM ADP-HPD, 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: 3→30 Å / Num. obs: 35972 / % possible obs: 90.1 %
Reflection shellResolution: 3→3.08 Å / % possible all: 97.5

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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: 3→30 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.902 / SU B: 60.053 / SU ML: 0.474 / Cross valid method: THROUGHOUT / ESU R Free: 0.5 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27378 1946 5.1 %RANDOM
Rwork0.2455 ---
obs0.24694 35972 89.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 106.691 Å2
Baniso -1Baniso -2Baniso -3
1-4.44 Å20 Å20 Å2
2---9.08 Å20 Å2
3---4.64 Å2
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11847 0 105 0 11952
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212271
X-RAY DIFFRACTIONr_bond_other_d0.0040.028049
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.9616773
X-RAY DIFFRACTIONr_angle_other_deg1.124319581
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.37151560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.7623.596520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.157151774
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7461572
X-RAY DIFFRACTIONr_chiral_restr0.0710.21865
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02113901
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022588
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: 3→3.081 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 141 -
Rwork0.297 2677 -
obs--97.54 %
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)
11.3795-1.03680.32026.2532-0.12031.0588-0.15840.02540.47620.3885-0.15920.1577-0.0971-0.14090.31770.26640.0242-0.11840.26-0.12410.305848.046231.60825.8255
22.96972.8213-0.06247.2940.90671.5620.1354-0.6695-0.1405-0.2857-0.6264-0.40570.0861-0.04430.4910.4158-0.0512-0.14050.48040.03220.385788.0632.356119.4844
31.4583-2.26760.57837.6228-1.19532.85620.63440.6283-0.3528-1.0266-0.62850.59340.57760.2277-0.00590.44960.2572-0.21220.5806-0.11520.137886.7766-27.749636.0505
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A438 - 958
2X-RAY DIFFRACTION2B438 - 958
3X-RAY DIFFRACTION3C438 - 958

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