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- PDB-6g28: Human [protein ADP-ribosylargenine] hydrolase ARH1 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6g28
TitleHuman [protein ADP-ribosylargenine] hydrolase ARH1 in complex with ADP-ribose
Components[Protein ADP-ribosylarginine] hydrolase
KeywordsHYDROLASE / ADP-ribosylation / ADP-ribose / ADPRH / ADP-ribosylhydrolase / ARH1
Function / homology
Function and homology information


[protein ADP-ribosylarginine] hydrolase / ADP-ribosylarginine hydrolase activity / protein de-ADP-ribosylation / potassium ion binding / protein modification process / magnesium ion binding / extracellular space
Similarity search - Function
ADP-ribosylarginine hydrolase / 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 ARH1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsAriza, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust101794 United Kingdom
CitationJournal: Cell Chem Biol / Year: 2018
Title: (ADP-ribosyl)hydrolases: Structural Basis for Differential Substrate Recognition and Inhibition.
Authors: Rack, J.G.M. / Ariza, A. / Drown, B.S. / Henfrey, C. / Bartlett, E. / Shirai, T. / Hergenrother, P.J. / Ahel, I.
History
DepositionMar 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: 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 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: [Protein ADP-ribosylarginine] hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3997
Polymers40,6851
Non-polymers7146
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-54 kcal/mol
Surface area13500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.102, 66.687, 83.420
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 [Protein ADP-ribosylarginine] hydrolase / ADP-ribosylarginine hydrolase / ADP-ribose-L-arginine cleaving enzyme


Mass: 40684.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADPRH, ARH1 / Production host: Escherichia coli (E. coli)
References: UniProt: P54922, [protein ADP-ribosylarginine] hydrolase
#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.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 200 mM magnesium formate, 20 % (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.23→66.69 Å / Num. obs: 103868 / % possible obs: 99.6 % / Redundancy: 12.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.025 / Rrim(I) all: 0.064 / Net I/σ(I): 21.7
Reflection shellResolution: 1.23→1.25 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 5.5 / Num. unique obs: 4932 / CC1/2: 0.981 / Rpim(I) all: 0.132 / Rrim(I) all: 0.295 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HFW

3hfw


Resolution: 1.23→52.09 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.158 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15744 5034 4.9 %RANDOM
Rwork0.14506 ---
obs0.14566 98756 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.97 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20 Å2-0 Å2
2---0.57 Å20 Å2
3----0.45 Å2
Refinement stepCycle: 1 / Resolution: 1.23→52.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2794 0 41 347 3182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0143072
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172652
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.6664178
X-RAY DIFFRACTIONr_angle_other_deg1.1181.6486240
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3055399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9322.086163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53615501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8971518
X-RAY DIFFRACTIONr_chiral_restr0.0890.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023527
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02624
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_it0.5730.9851477
X-RAY DIFFRACTIONr_mcbond_other0.5640.9841476
X-RAY DIFFRACTIONr_mcangle_it0.9111.4811855
X-RAY DIFFRACTIONr_mcangle_other0.9141.4821856
X-RAY DIFFRACTIONr_scbond_it0.9731.1341595
X-RAY DIFFRACTIONr_scbond_other0.9711.1341594
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5131.6582303
X-RAY DIFFRACTIONr_long_range_B_refined3.08312.4263759
X-RAY DIFFRACTIONr_long_range_B_other2.79911.8953672
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.23→1.262 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.189 362 -
Rwork0.183 7018 -
obs--97.17 %
Refinement TLS params.Method: refined / Origin x: 12.109 Å / Origin y: -1.081 Å / Origin z: -11.461 Å
111213212223313233
T0.0277 Å20.0153 Å2-0.0197 Å2-0.0173 Å2-0.0153 Å2--0.0318 Å2
L0.8079 °20.5213 °20.3422 °2-1.9327 °20.6185 °2--0.945 °2
S0.0136 Å °0.0184 Å °-0.1003 Å °0.1625 Å °0.1113 Å °-0.2052 Å °0.0675 Å °0.1119 Å °-0.125 Å °

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