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- PDB-7l9h: Crystal structure of human ARH3-D77A bound to magnesium and ADP-ribose -

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Basic information

Entry
Database: PDB / ID: 7l9h
TitleCrystal structure of human ARH3-D77A bound to magnesium and ADP-ribose
ComponentsADP-ribose glycohydrolase ARH3
KeywordsHYDROLASE / ADP-ribose / magnesium
Function / homology
Function and homology information


cellular response to superoxide / peptidyl-serine ADP-deribosylation / ADP-ribosylserine hydrolase activity / O-acetyl-ADP-ribose deacetylase activity / poly(ADP-ribose) glycohydrolase activity / poly(ADP-ribose) glycohydrolase / negative regulation of necroptotic process / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / site of DNA damage ...cellular response to superoxide / peptidyl-serine ADP-deribosylation / ADP-ribosylserine hydrolase activity / O-acetyl-ADP-ribose deacetylase activity / poly(ADP-ribose) glycohydrolase activity / poly(ADP-ribose) glycohydrolase / negative regulation of necroptotic process / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / site of DNA damage / POLB-Dependent Long Patch Base Excision Repair / hydrolase activity, hydrolyzing O-glycosyl compounds / base-excision repair, gap-filling / nuclear body / mitochondrial matrix / DNA repair / magnesium ion binding / mitochondrion / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
ADP-ribosylation/Crystallin J1 / ADP-ribosylglycohydrolase / ADP-ribosylation/Crystallin J1 superfamily / :
Similarity search - Domain/homology
Chem-AR6 / ADP-ribosylhydrolase ARH3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPourfarjam, Y. / Kurinov, I. / Moss, J. / Kim, I.K.
Funding support United States, 1items
OrganizationGrant numberCountry
American Cancer Society133405-RSG-19-200-01-DMC United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural and biochemical analysis of human ADP-ribosyl-acceptor hydrolase 3 reveals the basis of metal selectivity and different roles for the two magnesium ions.
Authors: Pourfarjam, Y. / Ma, Z. / Kurinov, I. / Moss, J. / Kim, I.K.
History
DepositionJan 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: ADP-ribose glycohydrolase ARH3
D: ADP-ribose glycohydrolase ARH3
A: ADP-ribose glycohydrolase ARH3
B: ADP-ribose glycohydrolase ARH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,27012
Polymers156,9364
Non-polymers2,3348
Water16,376909
1
C: ADP-ribose glycohydrolase ARH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8183
Polymers39,2341
Non-polymers5842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
D: ADP-ribose glycohydrolase ARH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8183
Polymers39,2341
Non-polymers5842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: ADP-ribose glycohydrolase ARH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8183
Polymers39,2341
Non-polymers5842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: ADP-ribose glycohydrolase ARH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8183
Polymers39,2341
Non-polymers5842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.702, 71.611, 115.928
Angle α, β, γ (deg.)94.238, 94.583, 107.619
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALATYRTYR(chain 'A' and (resid 14 through 39 or (resid 40...AC14 - 4017 - 43
12LEULEUHISHIS(chain 'A' and (resid 14 through 39 or (resid 40...AC48 - 5451 - 57
13GLUGLUPHEPHE(chain 'A' and (resid 14 through 39 or (resid 40...AC71 - 36074 - 363
14AR6AR6AR6AR6(chain 'A' and (resid 14 through 39 or (resid 40...AI401
21ALAALATYRTYR(chain 'B' and (resid 14 through 38 or (resid 39...BD14 - 4017 - 43
22LEULEUHISHIS(chain 'B' and (resid 14 through 38 or (resid 39...BD48 - 5451 - 57
23GLUGLUPHEPHE(chain 'B' and (resid 14 through 38 or (resid 39...BD71 - 36074 - 363
24AR6AR6AR6AR6(chain 'B' and (resid 14 through 38 or (resid 39...BK401
31ALAALATYRTYR(chain 'C' and (resid 14 through 41 or resid 48...CA14 - 4017 - 43
32LEULEUHISHIS(chain 'C' and (resid 14 through 41 or resid 48...CA48 - 5451 - 57
33GLUGLUPHEPHE(chain 'C' and (resid 14 through 41 or resid 48...CA71 - 36074 - 363
34AR6AR6AR6AR6(chain 'C' and (resid 14 through 41 or resid 48...CE401
41ALAALATYRTYR(chain 'D' and (resid 14 through 38 or (resid 39...DB14 - 4017 - 43
42LEULEUHISHIS(chain 'D' and (resid 14 through 38 or (resid 39...DB48 - 5451 - 57
43GLUGLUPHEPHE(chain 'D' and (resid 14 through 38 or (resid 39...DB71 - 36074 - 363
44AR6AR6AR6AR6(chain 'D' and (resid 14 through 38 or (resid 39...DG401

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Components

#1: Protein
ADP-ribose glycohydrolase ARH3 / ADP-ribosylhydrolase 3 / O-acetyl-ADP-ribose deacetylase ARH3 / Poly(ADP-ribose) glycohydrolase ...ADP-ribosylhydrolase 3 / O-acetyl-ADP-ribose deacetylase ARH3 / Poly(ADP-ribose) glycohydrolase ARH3 / [Protein ADP-ribosylarginine] hydrolase-like protein 2 / [Protein ADP-ribosylserine] hydrolase


Mass: 39233.949 Da / Num. of mol.: 4 / Mutation: D77A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADPRS, ADPRHL2, ARH3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NX46, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides, poly(ADP-ribose) glycohydrolase, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical
ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 909 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.23 Å3/Da / Density % sol: 44.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate buffer pH 4.5, 0.1 M MgCl2, and 22 % polyethylene glycol (PEG) 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.85→61.29 Å / Num. obs: 103770 / % possible obs: 89.5 % / Redundancy: 1.9 % / Biso Wilson estimate: 18.25 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 8.32
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 10511

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6D36

6d36


Resolution: 1.85→61.29 Å / SU ML: 0.2096 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 23.0105 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2273 5276 5.08 %
Rwork0.1801 98500 -
obs0.1825 103776 89.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.78 Å2
Refinement stepCycle: LAST / Resolution: 1.85→61.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9845 0 148 909 10902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012110167
X-RAY DIFFRACTIONf_angle_d1.236813798
X-RAY DIFFRACTIONf_chiral_restr0.05721566
X-RAY DIFFRACTIONf_plane_restr0.00851788
X-RAY DIFFRACTIONf_dihedral_angle_d8.54176025
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.30511570.22323350X-RAY DIFFRACTION91.26
1.87-1.890.29131670.22123324X-RAY DIFFRACTION91.05
1.89-1.920.27851760.22333334X-RAY DIFFRACTION90.58
1.92-1.940.27741850.20913392X-RAY DIFFRACTION90.74
1.94-1.970.23211390.20223315X-RAY DIFFRACTION91.25
1.97-1.990.26141700.20213357X-RAY DIFFRACTION90.67
1.99-2.020.24191730.19113305X-RAY DIFFRACTION89.82
2.02-2.050.23681770.19453262X-RAY DIFFRACTION89.05
2.05-2.080.26271520.20093253X-RAY DIFFRACTION88.58
2.08-2.120.25271850.19233258X-RAY DIFFRACTION88.08
2.12-2.150.24141730.1873099X-RAY DIFFRACTION85.34
2.15-2.190.24721610.17972966X-RAY DIFFRACTION79.87
2.19-2.240.23071790.18413442X-RAY DIFFRACTION92.82
2.24-2.280.25411860.18433274X-RAY DIFFRACTION91.61
2.28-2.330.24471950.18263397X-RAY DIFFRACTION92.24
2.33-2.390.23752160.17723363X-RAY DIFFRACTION92.05
2.39-2.440.2121620.17793340X-RAY DIFFRACTION91.32
2.44-2.510.23481780.17193339X-RAY DIFFRACTION91.21
2.51-2.580.2421720.17253313X-RAY DIFFRACTION90.17
2.58-2.670.2231970.17553247X-RAY DIFFRACTION88.51
2.67-2.760.21551550.17443111X-RAY DIFFRACTION84.22
2.76-2.870.22021650.18112995X-RAY DIFFRACTION82.42
2.87-30.24652160.17873419X-RAY DIFFRACTION93.49
3-3.160.21741810.17423391X-RAY DIFFRACTION93
3.16-3.360.22241940.16913329X-RAY DIFFRACTION91.1
3.36-3.620.22131350.16893383X-RAY DIFFRACTION90.67
3.62-3.990.18781440.15153149X-RAY DIFFRACTION84.74
3.99-4.560.16331880.14953179X-RAY DIFFRACTION87.48
4.56-5.750.20831970.16943388X-RAY DIFFRACTION93.26
5.75-61.290.25072010.21833226X-RAY DIFFRACTION88.28

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