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- PDB-4fc2: Crystal structure of mouse poly(ADP-ribose) glycohydrolase (PARG)... -

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Basic information

Entry
Database: PDB / ID: 4fc2
TitleCrystal structure of mouse poly(ADP-ribose) glycohydrolase (PARG) catalytic domain
ComponentsPoly(ADP-ribose) glycohydrolase
KeywordsHYDROLASE / mouse / PARG / poly(ADP-ribose) glycohydrolase
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 / SAD / Resolution: 1.91 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
DepositionMay 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _entity.formula_weight
Revision 1.3Oct 17, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _entity.formula_weight
Revision 1.4Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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
C: Poly(ADP-ribose) glycohydrolase
D: Poly(ADP-ribose) glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,74032
Polymers242,0504
Non-polymers2,69028
Water26,3201461
1
A: Poly(ADP-ribose) glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1858
Polymers60,5131
Non-polymers6727
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Poly(ADP-ribose) glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1858
Polymers60,5131
Non-polymers6727
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Poly(ADP-ribose) glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1858
Polymers60,5131
Non-polymers6727
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Poly(ADP-ribose) glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1858
Polymers60,5131
Non-polymers6727
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.141, 90.401, 104.696
Angle α, β, γ (deg.)81.640, 88.410, 89.360
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Poly(ADP-ribose) glycohydrolase


Mass: 60512.582 Da / Num. of mol.: 4 / Fragment: unp residues 439-959
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.: 28 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1461 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 52.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2M (NH4)2SO4, 16% PEG3,350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 31, 2012
RadiationMonochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. all: 187938 / Num. obs: 173052 / % possible obs: 92.1 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5
Reflection shellResolution: 1.91→1.98 Å / % possible all: 54.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0110refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.91→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.97 / SU B: 7.613 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2144 8659 5 %RANDOM
Rwork0.1739 ---
obs0.1759 173052 92.08 %-
all-187938 --
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: 81.22 Å2 / Biso mean: 38.528 Å2 / Biso min: 15.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20.07 Å2-0.88 Å2
2---0.6 Å20.71 Å2
3---0.79 Å2
Refinement stepCycle: LAST / Resolution: 1.91→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16481 0 140 1461 18082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02217006
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211909
X-RAY DIFFRACTIONr_angle_refined_deg1.1231.96723032
X-RAY DIFFRACTIONr_angle_other_deg0.834328798
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.74752023
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19523.103812
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.066152946
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.16115144
X-RAY DIFFRACTIONr_chiral_restr0.0670.22453
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02118626
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023618
X-RAY DIFFRACTIONr_mcbond_it1.473410148
X-RAY DIFFRACTIONr_mcbond_other0.45144069
X-RAY DIFFRACTIONr_mcangle_it2.313616421
X-RAY DIFFRACTIONr_scbond_it3.01266858
X-RAY DIFFRACTIONr_scangle_it4.509106611
LS refinement shellResolution: 1.913→1.963 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 378 -
Rwork0.253 6775 -
all-7153 -
obs--51.49 %
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)
11.0778-0.25030.66920.6276-0.18131.3430.0560.00640.0023-0.0905-0.03360.051-0.0599-0.0713-0.02240.03330.01310.00750.0163-0.01240.037316.117695.2721118.2572
21.1430.26420.69050.54850.16981.40270.0583-0.02410.03060.0963-0.0431-0.0417-0.05360.0439-0.01520.0356-0.01480.01520.0075-0.00150.042666.573534.934962.349
31.1050.2135-0.71330.4753-0.20791.3440.0454-0.0245-0.04950.0686-0.0426-0.01510.0426-0.0268-0.00270.033-0.0185-0.01060.0154-0.00370.023546.73884.059762.4007
41.033-0.1745-0.6110.60930.04571.40590.05220.0241-0.0539-0.0915-0.06-0.05060.10790.10020.00790.03510.0270.00070.02150.00140.042235.818353.9993118.3609
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A442 - 957
2X-RAY DIFFRACTION1A1001 - 1007
3X-RAY DIFFRACTION1A1101 - 1478
4X-RAY DIFFRACTION2B442 - 957
5X-RAY DIFFRACTION2B1001 - 1007
6X-RAY DIFFRACTION2B1101 - 1454
7X-RAY DIFFRACTION3C442 - 957
8X-RAY DIFFRACTION3C1001 - 1007
9X-RAY DIFFRACTION3C1101 - 1491
10X-RAY DIFFRACTION4D441 - 957
11X-RAY DIFFRACTION4D1001 - 1007
12X-RAY DIFFRACTION4D1101 - 1438

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