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- PDB-4j5s: TARG1 (C6orf130), Terminal ADP-ribose Glycohydrolase 1 ADP-ribose... -

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Basic information

Entry
Database: PDB / ID: 4j5s
TitleTARG1 (C6orf130), Terminal ADP-ribose Glycohydrolase 1 ADP-ribose complex
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
BORATE ION / 1,3,2-DIOXABOROLAN-2-OL / Chem-ZZC / ADP-ribose glycohydrolase OARD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 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

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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
C: O-acetyl-ADP-ribose deacetylase 1
D: O-acetyl-ADP-ribose deacetylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,20933
Polymers65,5564
Non-polymers3,65329
Water11,782654
1
A: O-acetyl-ADP-ribose deacetylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,41710
Polymers16,3891
Non-polymers1,0289
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: O-acetyl-ADP-ribose deacetylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,48811
Polymers16,3891
Non-polymers1,09910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: O-acetyl-ADP-ribose deacetylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0905
Polymers16,3891
Non-polymers7014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: O-acetyl-ADP-ribose deacetylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2147
Polymers16,3891
Non-polymers8256
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.375, 56.221, 73.788
Angle α, β, γ (deg.)90.00, 94.47, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain B and ((resid 400 and name *A) or (resid 87 and (name CD or name CE or name NZ)))
21chain C and ((resid 400 and name *A) or (resid 87 and (name CD or name CE or name NZ)))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain B and ((resid 400 and name *'A) or (resid 87 and (name CD or name CE or name NZ)))B0
211chain C and ((resid 400 and name *'A) or (resid 87 and (name CD or name CE or name NZ)))C0

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
O-acetyl-ADP-ribose deacetylase 1


Mass: 16389.080 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OARD1, C6orf130 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q9Y530, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

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Non-polymers , 6 types, 683 molecules

#2: Chemical
ChemComp-ZZC / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [[(2R,3R)-2,3-DIHYDROXY-4-OXO-PENTOXY]-OXIDO-PHOSPHORYL] PHOSPHATE


Mass: 541.300 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H21N5O13P2
#3: Chemical ChemComp-BO4 / BORATE ION


Mass: 78.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BH4O4
#4: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-SBE / 1,3,2-DIOXABOROLAN-2-OL


Mass: 87.870 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5BO3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 654 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsLYS 87 REACTS WITH THE C1 POSITION OF ADP-RIBOSE. FOLLOWING DEHYDRATION, AN IMINE INTERMEDIATE ...LYS 87 REACTS WITH THE C1 POSITION OF ADP-RIBOSE. FOLLOWING DEHYDRATION, AN IMINE INTERMEDIATE CONVERTS TO FORM A 2CC- KETOAMINE, VIA AN AMADORI REARRANGEMENT (CERVANTES-LAUREAN ET AL, 1993), AND SIMILAR TO THAT OBSERVED IN THE X-RAY STRUCTURE OF DRAG-ADP-RIBOSE COMPLEX (BERTHOLD ET AL, 2009).

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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: 2.31 Å3/Da / Density % sol: 46.86 %
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-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 25, 2011
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 86974 / Num. obs: 85148 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.043 / Χ2: 1.041 / Net I/σ(I): 11.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.55-1.583.80.53441641.032196.2
1.58-1.613.80.46841601.035196
1.61-1.643.90.40442181.03197.2
1.64-1.673.90.33141670.992196.6
1.67-1.713.90.2942081.026196.8
1.71-1.753.90.24942071.02197.1
1.75-1.793.90.21442071.042197.3
1.79-1.843.90.17242091.085197.6
1.84-1.893.90.14642221.125197.6
1.89-1.953.80.12142191.323197.6
1.95-2.023.90.09642341.217198
2.02-2.13.80.07642811.24198.1
2.1-2.23.90.06342661.217198.5
2.2-2.323.80.05742981.208198.5
2.32-2.463.90.05142541.19198.3
2.46-2.653.80.04643321.11199.3
2.65-2.923.90.03843251.007199
2.92-3.343.80.02943440.987199.1
3.34-4.213.80.02343790.487199.6
4.21-503.70.02444540.439199

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→38.953 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8995 / SU ML: 0.14 / σ(F): 1.34 / Phase error: 16.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.175 4291 5.04 %RANDOM
Rwork0.137 ---
obs0.139 85113 97.69 %-
all-86974 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.59 Å2 / Biso mean: 25.2064 Å2 / Biso min: 8.87 Å2
Refinement stepCycle: LAST / Resolution: 1.55→38.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4457 0 226 654 5337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085223
X-RAY DIFFRACTIONf_angle_d1.1857044
X-RAY DIFFRACTIONf_chiral_restr0.065773
X-RAY DIFFRACTIONf_plane_restr0.005883
X-RAY DIFFRACTIONf_dihedral_angle_d18.3112062
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B22X-RAY DIFFRACTIONPOSITIONAL0.004
12C22X-RAY DIFFRACTIONPOSITIONAL0.004
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5499-1.56750.25491470.17472520266791
1.5675-1.5860.2231560.16722589274597
1.586-1.60530.22591290.15672630275996
1.6053-1.62560.2021390.14912653279297
1.6256-1.6470.22281440.142646279097
1.647-1.66960.19951420.13862661280397
1.6696-1.69340.18841530.13622652280597
1.6934-1.71870.22641400.1342678281897
1.7187-1.74560.21390.12592651279097
1.7456-1.77420.2061540.12072635278997
1.7742-1.80480.15221410.12022663280497
1.8048-1.83760.17641270.11742719284698
1.8376-1.87290.18631380.11992660279897
1.8729-1.91120.17221490.11852668281798
1.9112-1.95270.18141290.12622714284398
1.9527-1.99820.20581400.12892713285398
1.9982-2.04810.18461420.12312704284699
2.0481-2.10350.15911410.11772700284198
2.1035-2.16540.17041550.12362697285298
2.1654-2.23530.14751590.11932685284499
2.2353-2.31520.17361600.1232720288099
2.3152-2.40780.17031400.13122684282499
2.4078-2.51740.19051220.13452774289699
2.5174-2.65010.18341420.13542748289099
2.6501-2.81610.15761420.14492731287399
2.8161-3.03350.17391270.146827612888100
3.0335-3.33860.18761490.14042770291999
3.3386-3.82130.16431540.13842760291499
3.8213-4.8130.14151460.130627892935100
4.813-38.96490.18681450.17172847299299

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