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- PDB-4b1h: Structure of human PARG catalytic domain in complex with ADP-ribose -

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Basic information

Entry
Database: PDB / ID: 4b1h
TitleStructure of human PARG catalytic domain in complex with ADP-ribose
ComponentsPOLY(ADP-RIBOSE) GLYCOHYDROLASEPoly(ADP-ribose) glycohydrolase
KeywordsHYDROLASE
Function / homology
Function and homology information


nucleotide-sugar metabolic process / poly(ADP-ribose) glycohydrolase / poly(ADP-ribose) glycohydrolase activity / ATP generation from poly-ADP-D-ribose / POLB-Dependent Long Patch Base Excision Repair / regulation of DNA repair / base-excision repair, gap-filling / nuclear body / carbohydrate metabolic process / mitochondrial matrix ...nucleotide-sugar metabolic process / poly(ADP-ribose) glycohydrolase / poly(ADP-ribose) glycohydrolase activity / ATP generation from poly-ADP-D-ribose / POLB-Dependent Long Patch Base Excision Repair / regulation of DNA repair / base-excision repair, gap-filling / nuclear body / carbohydrate metabolic process / mitochondrial matrix / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Poly (ADP-ribose) glycohydrolase (PARG), helical domain / Poly (ADP-ribose) glycohydrolase (PARG), catalytic domain / Poly(ADP-ribose) glycohydrolase / Poly (ADP-ribose) glycohydrolase (PARG), Macro domain fold
Similarity search - Domain/homology
Chem-AR6 / BETA-MERCAPTOETHANOL / (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Poly(ADP-ribose) glycohydrolase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBrassington, C. / Ellston, J. / Hassall, G. / Holdgate, G. / McAlister, M. / Smith, G. / Tucker, J.A. / Watson, M.
CitationJournal: Plos One / Year: 2012
Title: Structures of the Human Poly (Adp-Ribose) Glycohydrolase Catalytic Domain Confirm Catalytic Mechanism and Explain Inhibition by Adp-Hpd Derivatives.
Authors: Tucker, J.A. / Bennett, N. / Brassington, C. / Durant, S.T. / Hassall, G. / Holdgate, G. / Mcalister, M. / Nissink, J.W.M. / Truman, C. / Watson, M.
History
DepositionJul 10, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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 / _struct_conn.ptnr2_label_seq_id / _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: POLY(ADP-RIBOSE) GLYCOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6889
Polymers60,9601
Non-polymers1,7278
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.929, 90.656, 94.975
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein POLY(ADP-RIBOSE) GLYCOHYDROLASE / Poly(ADP-ribose) glycohydrolase


Mass: 60960.258 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 448-976 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28A-6HIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD
References: UniProt: Q86W56, poly(ADP-ribose) glycohydrolase

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Non-polymers , 6 types, 386 molecules

#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-DTV / (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: 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.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsDTV: DTT FROM PROTEIN BUFFER DERIVATISES CYSTEINE TO FORM (2R)-2-AZANIUMYL-3-[[(2S,3S)-2,3- ...DTV: DTT FROM PROTEIN BUFFER DERIVATISES CYSTEINE TO FORM (2R)-2-AZANIUMYL-3-[[(2S,3S)-2,3-DIHYDROXY-4-SULFANYL] PROPANOATE
Sequence detailsCODON OPTIMISED SEQUENCE, SIX MUTATIONS INTRODUCED TO ENHANCE CRYSTALLISABILITY ...CODON OPTIMISED SEQUENCE, SIX MUTATIONS INTRODUCED TO ENHANCE CRYSTALLISABILITY K617A,Q618A,K619A,E688A,K689A, K690A

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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: 2.48 Å3/Da / Density % sol: 50.47 % / Description: NONE
Crystal growDetails: 25% PEG 3350, 36.4MM PCTP-4, 63.6MM PCTP-10, 0.2M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 16, 2009 / Details: VARIMAXHF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→27.54 Å / Num. obs: 39298 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 6.15 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.84 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.5 / % possible all: 90.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A0D

4a0d


Resolution: 2→27.35 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 8.39 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24139 1961 5 %RANDOM
Rwork0.20356 ---
obs0.20548 37234 98.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.098 Å2
Baniso -1Baniso -2Baniso -3
1--1.31 Å20 Å20 Å2
2--0.46 Å20 Å2
3---0.85 Å2
Refinement stepCycle: LAST / Resolution: 2→27.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4071 0 81 378 4530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.024346
X-RAY DIFFRACTIONr_bond_other_d0.0020.022983
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.955909
X-RAY DIFFRACTIONr_angle_other_deg2.26237220
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.3885.05528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26123.1203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.4715716
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.111536
X-RAY DIFFRACTIONr_chiral_restr0.0950.2635
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024832
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02933
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_it0.7621.52595
X-RAY DIFFRACTIONr_mcbond_other0.1961.51041
X-RAY DIFFRACTIONr_mcangle_it1.35624199
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.13131751
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2894.51710
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 135 -
Rwork0.35 2470 -
obs--89.61 %
Refinement TLS params.Method: refined / Origin x: 17.9681 Å / Origin y: 2.8058 Å / Origin z: 8.4344 Å
111213212223313233
T0.0321 Å2-0.0004 Å2-0.0108 Å2-0.0797 Å2-0.009 Å2--0.0055 Å2
L0.7722 °2-0.2279 °2-0.0521 °2-1.1207 °2-0.0965 °2--0.3504 °2
S-0.0191 Å °-0.0829 Å °-0.0036 Å °0.0507 Å °0.0384 Å °-0.0014 Å °0.0457 Å °0.0103 Å °-0.0193 Å °

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