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- PDB-4j5r: TARG1 (C6orf130), Terminal ADP-ribose Glycohydrolase 1 bound to A... -

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Basic information

Entry
Database: PDB / ID: 4j5r
TitleTARG1 (C6orf130), Terminal ADP-ribose Glycohydrolase 1 bound to ADP-HPD
ComponentsO-acetyl-ADP-ribose deacetylase 1
KeywordsHYDROLASE / DNA repair / Cellular signaling / macro domain / glycohydrolase / poly-ADP ribose / PARP / ADP-ribose
Function / homology
Function and homology information


ADP-ribosylglutamate hydrolase activity / protein de-ADP-ribosylation / peptidyl-glutamate ADP-deribosylation / purine nucleoside metabolic process / purine nucleoside binding / O-acetyl-ADP-ribose deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / site of DNA damage / DNA damage response ...ADP-ribosylglutamate hydrolase activity / protein de-ADP-ribosylation / peptidyl-glutamate ADP-deribosylation / purine nucleoside metabolic process / purine nucleoside binding / O-acetyl-ADP-ribose deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / site of DNA damage / DNA damage response / nucleolus / nucleoplasm
Similarity search - Function
Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-A1R / ADP-ribose glycohydrolase OARD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsSchellenberg, M.J. / Appel, C.D. / Krahn, J. / Williams, R.S.
CitationJournal: Embo J. / Year: 2013
Title: Deficiency of terminal ADP-ribose protein glycohydrolase TARG1/C6orf130 in neurodegenerative disease.
Authors: Sharifi, R. / Morra, R. / Appel, C.D. / Tallis, M. / Chioza, B. / Jankevicius, G. / Simpson, M.A. / Matic, I. / Ozkan, E. / Golia, B. / Schellenberg, M.J. / Weston, R. / Williams, J.G. / ...Authors: Sharifi, R. / Morra, R. / Appel, C.D. / Tallis, M. / Chioza, B. / Jankevicius, G. / Simpson, M.A. / Matic, I. / Ozkan, E. / Golia, B. / Schellenberg, M.J. / Weston, R. / Williams, J.G. / Rossi, M.N. / Galehdari, H. / Krahn, J. / Wan, A. / Trembath, R.C. / Crosby, A.H. / Ahel, D. / Hay, R. / Ladurner, A.G. / Timinszky, G. / Williams, R.S. / Ahel, I.
History
DepositionFeb 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2Jul 3, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: O-acetyl-ADP-ribose deacetylase 1
B: O-acetyl-ADP-ribose deacetylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,40414
Polymers32,7782
Non-polymers1,62512
Water10,683593
1
A: O-acetyl-ADP-ribose deacetylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1897
Polymers16,3891
Non-polymers7996
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: O-acetyl-ADP-ribose deacetylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2157
Polymers16,3891
Non-polymers8266
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-27 kcal/mol
Surface area13380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.803, 72.004, 81.919
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 O-acetyl-ADP-ribose deacetylase 1


Mass: 16389.080 Da / Num. of mol.: 2 / Fragment: unp residues 11-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OARD1, C6orf130 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y530, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#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.: 2 / Source method: obtained synthetically / Formula: C15H24N6O12P2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 593 / 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: 2.29 Å3/Da / Density % sol: 46.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100mM Imidazole, 20% PEG3350, 200 mM NaCl , pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 4, 2011
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. all: 83829 / Num. obs: 79051 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 5 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 7.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.25-1.273.80.402164.6
1.27-1.2940.397183.5
1.29-1.324.50.367191.1
1.32-1.354.80.325193.9
1.35-1.3850.335194.6
1.38-1.415.10.304195.6
1.41-1.445.20.24196.3
1.44-1.485.20.215196.2
1.48-1.535.20.181196.3
1.53-1.575.20.156196.6
1.57-1.635.20.135196.9
1.63-1.75.20.124197.1
1.7-1.775.20.107197.9
1.77-1.875.20.088197.5
1.87-1.985.20.076198.2
1.98-2.145.20.068198.2
2.14-2.355.20.069198.8
2.35-2.695.20.06198.9
2.69-3.395.20.046198.7
3.39-505.20.036194.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4J5Q

4j5q


Resolution: 1.25→43.17 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.978 / Occupancy max: 1 / Occupancy min: 0.02 / SU B: 1.158 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.15283 3940 5 %RANDOM
Rwork0.1183 ---
obs0.12008 75061 94.32 %-
all-83829 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.765 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å20 Å2
2---0.08 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.25→43.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2209 0 101 593 2903
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022730
X-RAY DIFFRACTIONr_bond_other_d0.0010.022799
X-RAY DIFFRACTIONr_angle_refined_deg1.8882.0353698
X-RAY DIFFRACTIONr_angle_other_deg0.9253.0046369
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2515348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.40823.818110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.38415548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3131520
X-RAY DIFFRACTIONr_chiral_restr0.6310.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022975
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02581
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_restr2.62435529
X-RAY DIFFRACTIONr_sphericity_free28.15120
X-RAY DIFFRACTIONr_sphericity_bonded10.755970
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 214 -
Rwork0.232 3922 -
obs--68.85 %

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