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- PDB-4na6: Crystal structure of mouse poly(ADP-ribose) glycohydrolase (PARG)... -

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Basic information

Entry
Database: PDB / ID: 4na6
TitleCrystal structure of mouse poly(ADP-ribose) glycohydrolase (PARG) catalytic domain mutant E749N
ComponentsPoly(ADP-ribose) glycohydrolase
KeywordsHYDROLASE / Poly(ADP-ribose) glycohydrolase / PARG
Function / homology
Function and homology information


POLB-Dependent Long Patch Base Excision Repair / poly(ADP-ribose) glycohydrolase activity / poly(ADP-ribose) glycohydrolase / ATP generation from poly-ADP-D-ribose / detection of bacterium / regulation of DNA repair / carbohydrate metabolic process / DNA damage response / nucleus / cytosol
Similarity search - Function
Poly(ADP-ribose) glycohydrolase / Poly (ADP-ribose) glycohydrolase (PARG), catalytic domain / : / Poly (ADP-ribose) glycohydrolase (PARG), Macro domain fold / Poly (ADP-ribose) glycohydrolase (PARG), helical domain
Similarity search - Domain/homology
Poly(ADP-ribose) glycohydrolase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsWang, Z. / Cheng, Z. / Xu, W.
CitationJournal: Plos One / Year: 2014
Title: Crystallographic and biochemical analysis of the mouse poly(ADP-ribose) glycohydrolase.
Authors: Wang, Z. / Gagne, J.P. / Poirier, G.G. / Xu, W.
History
DepositionOct 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)121,03410
Polymers120,2652
Non-polymers7698
Water00
1
A: Poly(ADP-ribose) glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5175
Polymers60,1331
Non-polymers3844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Poly(ADP-ribose) glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5175
Polymers60,1331
Non-polymers3844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.599, 66.978, 101.548
Angle α, β, γ (deg.)90.000, 98.000, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Poly(ADP-ribose) glycohydrolase


Mass: 60132.574 Da / Num. of mol.: 2 / Fragment: catalytic domain / Mutation: E749N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Parg / Production host: Escherichia coli (E. coli)
References: UniProt: O88622, poly(ADP-ribose) glycohydrolase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4

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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: 2.56 Å3/Da / Density % sol: 52.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2M (NH4)2SO4, 16% PEG 3,350, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 2, 2012
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 43004 / Num. obs: 40639 / % possible obs: 94.5 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Rmerge(I) obs: 0.091
Reflection shellResolution: 2.5→2.57 Å / % possible all: 59.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0110refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4FC2

4fc2


Resolution: 2.48→50 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.889 / Occupancy max: 1 / Occupancy min: 1 / SU B: 23.227 / SU ML: 0.232 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.678 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2551 2048 5 %RANDOM
Rwork0.2161 ---
obs0.2181 40627 93.82 %-
all-43303 --
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 max: 104.17 Å2 / Biso mean: 36.8776 Å2 / Biso min: 11.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å2-0.11 Å2
2---0.11 Å20 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.48→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8209 0 40 0 8249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0228446
X-RAY DIFFRACTIONr_angle_refined_deg0.9891.96311433
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.99751007
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.4123.103406
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.652151471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5471572
X-RAY DIFFRACTIONr_chiral_restr0.0670.21221
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216418
X-RAY DIFFRACTIONr_mcbond_it0.96145049
X-RAY DIFFRACTIONr_mcangle_it1.80568168
X-RAY DIFFRACTIONr_scbond_it2.1963397
X-RAY DIFFRACTIONr_scangle_it3.584103265
LS refinement shellResolution: 2.484→2.549 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 86 -
Rwork0.306 1575 -
all-1661 -
obs--52.58 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7484-0.12350.01151.518-0.77871.5903-0.053-0.1792-0.1080.05940.0161-0.07510.1460.09230.03690.03070.02370.00390.08570.00450.0342-40.7828-10.8639-27.5785
20.68160.19330.02741.3680.60312.19280.0176-0.10680.16310.0953-0.03180.2664-0.2208-0.2630.01420.05060.03670.01360.090.00830.1489-81.91910.2208-25.5849
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A442 - 957
2X-RAY DIFFRACTION1A1001 - 1004
3X-RAY DIFFRACTION2B443 - 957
4X-RAY DIFFRACTION2B1001 - 1004

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