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- PDB-3sii: The X-ray crystal structure of poly(ADP-ribose) glycohydrolase bo... -

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Basic information

Entry
Database: PDB / ID: 3sii
TitleThe X-ray crystal structure of poly(ADP-ribose) glycohydrolase bound to the inhibitor ADP-HPD from Thermomonospora curvata
Componentspoly(ADP-ribose) glycohydrolase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


Conserved hypothetical protein CHP02452 / Microbial-type PARG, catalytic domain / Microbial-type PARG, catalytic domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Macro domain-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-A1R / Microbial-type PARG catalytic domain-containing protein
Similarity search - Component
Biological speciesThermomonospora curvata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsDunstan, M.S. / Leys, D.
CitationJournal: Nature / Year: 2011
Title: The structure and catalytic mechanism of a poly(ADP-ribose) glycohydrolase.
Authors: Slade, D. / Dunstan, M.S. / Barkauskaite, E. / Weston, R. / Lafite, P. / Dixon, N. / Ahel, M. / Leys, D. / Ahel, I.
History
DepositionJun 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Database references
Revision 1.2Oct 12, 2011Group: Database references
Revision 1.3Sep 13, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)30,3062
Polymers29,7641
Non-polymers5421
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.270, 44.220, 50.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein poly(ADP-ribose) glycohydrolase / PARG


Mass: 29763.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermomonospora curvata (bacteria) / Strain: ATCC 19995 / DSM 43183 / JCM 3096 / NCIMB 10081 / Gene: Tcur_1721 / Production host: Escherichia coli (E. coli)
References: UniProt: D1AC29, poly(ADP-ribose) glycohydrolase
#2: Chemical ChemComp-A1R / 5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE


Mass: 542.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N6O12P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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 Å3/Da / Density % sol: 38.44 %
Crystal growMethod: sitting drop, vapor diffusion / pH: 9
Details: 10% PEG6000, 0.1 M Bicine, pH 9.0, SITTING DROP, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.976
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.392→31.688 Å / Num. all: 44399 / Num. obs: 44385 / % possible obs: 99.7 %

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SIH

3sih


Resolution: 1.48→31.688 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8975 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 17.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1964 1975 5.01 %RANDOM
Rwork0.1634 ---
obs0.165 44385 99.7 %-
all-44399 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.901 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso max: 83.64 Å2 / Biso mean: 20.3848 Å2 / Biso min: 7.01 Å2
Baniso -1Baniso -2Baniso -3
1-2.1917 Å2-0 Å2-0 Å2
2---0.8951 Å20 Å2
3----1.2966 Å2
Refine analyzeLuzzati sigma a obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.48→31.688 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2028 0 35 333 2396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062116
X-RAY DIFFRACTIONf_angle_d1.1152878
X-RAY DIFFRACTIONf_chiral_restr0.067310
X-RAY DIFFRACTIONf_plane_restr0.004380
X-RAY DIFFRACTIONf_dihedral_angle_d19.221789
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.48-1.5170.29931240.24362109223378
1.517-1.5580.29711410.2262380252189
1.558-1.60390.24721120.21482629274197
1.6039-1.65570.23831600.18222674283499
1.6557-1.71480.2021300.18342744287499
1.7148-1.78350.21041710.170326882859100
1.7835-1.86460.18271250.15442713283899
1.8646-1.96290.17921470.154627212868100
1.9629-2.08590.1931600.157327302890100
2.0859-2.24690.17681310.155127522883100
2.2469-2.47290.18781440.156427702914100
2.4729-2.83060.20161400.167827812921100
2.8306-3.56550.18781360.160628202956100
3.5655-31.69480.18221540.14992914306899
Refinement TLS params.Method: refined / Origin x: 14.1093 Å / Origin y: -13.3999 Å / Origin z: -4.9954 Å
111213212223313233
T0.0634 Å2-0.008 Å2-0.0035 Å2-0.0753 Å2-0.005 Å2--0.0923 Å2
L0.8767 °20.0203 °2-0.4704 °2-0.569 °2-0.355 °2--1.0197 °2
S-0.0437 Å °-0.0073 Å °-0.0101 Å °-0.0694 Å °0.0086 Å °0.0223 Å °0.0602 Å °-0.0435 Å °0.026 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 1001
2X-RAY DIFFRACTION1allA1 - 333

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