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- PDB-5zqy: Crystal structure of a poly(ADP-ribose) glycohydrolase -

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Basic information

Entry
Database: PDB / ID: 5zqy
TitleCrystal structure of a poly(ADP-ribose) glycohydrolase
ComponentsPoly(ADP-ribose) glycohydrolase ARH3
KeywordsHYDROLASE / poly(ADP-ribose) glycohydrolase / LYASE
Function / homology
Function and homology information


ADP-ribosylserine hydrolase activity / peptidyl-serine ADP-deribosylation / cellular response to superoxide / O-acetyl-ADP-ribose deacetylase activity / poly(ADP-ribose) glycohydrolase / poly(ADP-ribose) glycohydrolase activity / 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 ...ADP-ribosylserine hydrolase activity / peptidyl-serine ADP-deribosylation / cellular response to superoxide / O-acetyl-ADP-ribose deacetylase activity / poly(ADP-ribose) glycohydrolase / poly(ADP-ribose) glycohydrolase activity / 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-ribosylglycohydrolase fold / ADP-ribosylation/Crystallin J1 / ADP-ribosylation/Crystallin J1 / ADP-ribosylglycohydrolase / ADP-ribosylation/Crystallin J1 superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-AR6 / ADP-ribosylhydrolase ARH3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.577 Å
AuthorsWang, M. / Yuan, Z. / Ma, Y. / Wang, J. / Liu, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China81672794 China
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structure-function analyses reveal the mechanism of the ARH3-dependent hydrolysis of ADP-ribosylation.
Authors: Wang, M. / Yuan, Z. / Xie, R. / Ma, Y. / Liu, X. / Yu, X.
History
DepositionApr 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poly(ADP-ribose) glycohydrolase ARH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4624
Polymers37,8541
Non-polymers6083
Water4,720262
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-19 kcal/mol
Surface area14000 Å2
Unit cell
Length a, b, c (Å)43.880, 76.740, 48.530
Angle α, β, γ (deg.)90.00, 103.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 37854.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADPRHL2, ARH3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NX46, poly(ADP-ribose) glycohydrolase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: 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.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.11 Å3/Da / Density % sol: 41.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: MES pH 6.0, PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.577→50 Å / Num. obs: 40881 / % possible obs: 96.4 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 15.8
Reflection shellResolution: 1.58→1.64 Å / Rmerge(I) obs: 0.207

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Processing

Software
NameVersionClassification
PHENIX(dev_3092)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FOZ

2foz


Resolution: 1.577→37.35 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 16.9
RfactorNum. reflection% reflection
Rfree0.1799 1986 4.86 %
Rwork0.1574 --
obs0.1585 40881 94.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.577→37.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2641 0 38 262 2941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062776
X-RAY DIFFRACTIONf_angle_d0.9183770
X-RAY DIFFRACTIONf_dihedral_angle_d5.282856
X-RAY DIFFRACTIONf_chiral_restr0.05415
X-RAY DIFFRACTIONf_plane_restr0.005497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.577-1.61640.2261150.17712191X-RAY DIFFRACTION76
1.6164-1.66010.21271420.16092741X-RAY DIFFRACTION94
1.6601-1.7090.20511410.1612807X-RAY DIFFRACTION96
1.709-1.76410.18821420.1572809X-RAY DIFFRACTION96
1.7641-1.82720.19311450.1572805X-RAY DIFFRACTION96
1.8272-1.90030.19751430.15782825X-RAY DIFFRACTION97
1.9003-1.98680.20961420.15852808X-RAY DIFFRACTION96
1.9868-2.09160.19551440.15472846X-RAY DIFFRACTION97
2.0916-2.22260.17051430.15012789X-RAY DIFFRACTION96
2.2226-2.39420.16011460.15632848X-RAY DIFFRACTION97
2.3942-2.63510.17731440.16852839X-RAY DIFFRACTION97
2.6351-3.01620.19081470.15862864X-RAY DIFFRACTION97
3.0162-3.79950.15971460.15122859X-RAY DIFFRACTION97
3.7995-37.36010.16511460.15642864X-RAY DIFFRACTION95

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