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- PDB-8rsm: Crystal structure of Streptococcus pyogenes macrodomain in comple... -

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Basic information

Entry
Database: PDB / ID: 8rsm
TitleCrystal structure of Streptococcus pyogenes macrodomain in complex with ADP-ribose
ComponentsProtein-ADP-ribose hydrolase
KeywordsHYDROLASE / ADP-RIBOSYLATION / ADP-RIBOSE / ADP-RIBOSYLHYDROLASE / Lipoylation / Metalloenzyme
Function / homologypoly(ADP-ribose) glycohydrolase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / Chem-AR6 / Protein-ADP-ribose hydrolase
Function and homology information
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsAriza, A.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Wellcome Trust210634 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R007195/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/W016613/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/X007472/1 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Evolutionary and molecular basis of ADP-ribosylation reversal by zinc-dependent macrodomains.
Authors: Ariza, A. / Liu, Q. / Cowieson, N.P. / Ahel, I. / Filippov, D.V. / Rack, J.G.M.
History
DepositionJan 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 16, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_volume / _citation_author.name / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein-ADP-ribose hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0493
Polymers30,4251
Non-polymers6252
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.704, 41.704, 137.895
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Protein-ADP-ribose hydrolase / SpyMacroD


Mass: 30424.736 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: SPy_1216, M5005_Spy0930 / Production host: Escherichia coli (E. coli)
References: UniProt: Q99ZI6, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.97 Å3/Da / Density % sol: 37.59 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 100 mM sodium cocadylate [pH 6.5], 27% (w/v) PEG2000MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.2822 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2822 Å / Relative weight: 1
ReflectionResolution: 1.87→68.95 Å / Num. obs: 19406 / % possible obs: 99.8 % / Redundancy: 6.6 % / CC1/2: 0.998 / Net I/σ(I): 12.6
Reflection shellResolution: 1.87→1.91 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1211 / CC1/2: 0.536 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→41.704 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.818 / SU ML: 0.091 / Cross valid method: FREE R-VALUE / ESU R: 0.138 / ESU R Free: 0.132
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.201 1005 5.193 %
Rwork0.1529 18347 -
all0.155 --
obs-19352 99.814 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 26.749 Å2
Baniso -1Baniso -2Baniso -3
1--0.903 Å20 Å20 Å2
2---0.903 Å2-0 Å2
3---1.806 Å2
Refinement stepCycle: LAST / Resolution: 1.87→41.704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1993 0 37 127 2157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122087
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161971
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.6642835
X-RAY DIFFRACTIONr_angle_other_deg0.561.5824539
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2165254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.655513
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.54854
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.98810353
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg19.904102
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.9891089
X-RAY DIFFRACTIONr_chiral_restr0.0780.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022401
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02475
X-RAY DIFFRACTIONr_nbd_refined0.2190.2433
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.21760
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21025
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21147
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2108
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.070.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2070.27
X-RAY DIFFRACTIONr_nbd_other0.230.234
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2650.210
X-RAY DIFFRACTIONr_mcbond_it2.2062.111016
X-RAY DIFFRACTIONr_mcbond_other2.2062.111016
X-RAY DIFFRACTIONr_mcangle_it3.3243.7641267
X-RAY DIFFRACTIONr_mcangle_other3.3253.7681268
X-RAY DIFFRACTIONr_scbond_it3.4282.5611071
X-RAY DIFFRACTIONr_scbond_other3.4272.561072
X-RAY DIFFRACTIONr_scangle_it5.1774.4941567
X-RAY DIFFRACTIONr_scangle_other5.1764.4941568
X-RAY DIFFRACTIONr_lrange_it6.93623.3132374
X-RAY DIFFRACTIONr_lrange_other6.91122.8692356
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.87-1.9190.238570.19313120.19514050.9610.96797.43770.175
1.919-1.9710.22710.18913480.1914190.9670.9721000.17
1.971-2.0280.241750.16612750.17113500.9640.9791000.148
2.028-2.090.213800.15912390.16313190.9720.9811000.143
2.09-2.1590.187660.15311860.15512520.9770.9841000.139
2.159-2.2340.203780.1511560.15312340.9750.9851000.136
2.234-2.3180.209510.13611640.1412150.9760.9881000.125
2.318-2.4130.147610.1310620.13111230.9830.9891000.122
2.413-2.5190.207550.14810560.15111110.9740.9871000.142
2.519-2.6420.176720.1459860.14810580.9790.9881000.139
2.642-2.7840.206580.1429510.14610090.9730.9881000.141
2.784-2.9520.191480.148950.1429430.9760.9881000.138
2.952-3.1550.198410.1488310.158720.9760.9871000.151
3.155-3.4060.186470.1547890.1568360.9760.9851000.162
3.406-3.7290.195330.1497460.1517790.9770.9881000.161
3.729-4.1650.215240.1486790.157030.9730.9881000.162
4.165-4.8010.176340.1445550.1465890.9870.9881000.161
4.801-5.8610.25180.1775110.1795290.9810.9861000.197
5.861-8.2080.222260.1683840.1724100.9720.9821000.186
8.208-41.7040.277100.172210.1742310.9740.9821000.197
Refinement TLS params.Method: refined / Origin x: -28.5989 Å / Origin y: 86.9473 Å / Origin z: -11.577 Å
111213212223313233
T0.0036 Å2-0.0041 Å2-0.0034 Å2-0.0093 Å20.004 Å2--0.0033 Å2
L0.7334 °2-0.0222 °2-0.1577 °2-0.5003 °2-0.2033 °2--0.9606 °2
S-0.0063 Å °-0.0052 Å °-0 Å °-0.0165 Å °0.0043 Å °0.0165 Å °-0.0054 Å °0.0132 Å °0.002 Å °
Refinement TLS groupSelection: ALL

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