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- PDB-8rsj: Crystal structure of Methanobrevibacter oralis macrodomain in com... -

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Basic information

Entry
Database: PDB / ID: 8rsj
TitleCrystal structure of Methanobrevibacter oralis macrodomain in complex with ADPr in open conformation
ComponentsO-acetyl-ADP-ribose deacetylase
KeywordsHYDROLASE / ADP-RIBOSYLATION / ADP-RIBOSE / ADP-RIBOSYLHYDROLASE / Lipoylation / Metalloenzyme
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / hydrolase activity / metal ion binding
Similarity search - Function
Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like
Similarity search - Domain/homology
Chem-JNT / Protein-ADP-ribose hydrolase
Similarity search - Component
Biological speciesMethanobrevibacter oralis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 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: O-acetyl-ADP-ribose deacetylase
B: O-acetyl-ADP-ribose deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6897
Polymers59,3442
Non-polymers1,3465
Water11,205622
1
A: O-acetyl-ADP-ribose deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2993
Polymers29,6721
Non-polymers6272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: O-acetyl-ADP-ribose deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3914
Polymers29,6721
Non-polymers7193
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.986, 58.101, 76.269
Angle α, β, γ (deg.)90.000, 117.664, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein O-acetyl-ADP-ribose deacetylase / Methonobrevibacter oralis macrodomain


Mass: 29671.775 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanobrevibacter oralis (archaea) / Gene: ymdB, MBORA_13990 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A166ACJ5, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-JNT / [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{S})-2,3,4,5-tetrakis(oxidanyl)pentyl] hydrogen phosphate


Mass: 561.332 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H25N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 622 / 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: 2.51 Å3/Da / Density % sol: 51.05 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 200 mM sodium fluoride, 100 mM BisTris propane [pH 7.5], 20% (w/v) PEG3350< 1 M potassium sodium tartrate tetrahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.66→67.39 Å / Num. obs: 68604 / % possible obs: 98.5 % / Redundancy: 6 % / CC1/2: 0.999 / Net I/σ(I): 18.7
Reflection shellResolution: 1.66→1.69 Å / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2906 / CC1/2: 0.873

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→67.39 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.814 / SU ML: 0.084 / Cross valid method: FREE R-VALUE / ESU R: 0.111 / ESU R Free: 0.111
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2319 3322 4.844 %
Rwork0.1921 65261 -
all0.194 --
obs-68583 98.34 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 24.098 Å2
Baniso -1Baniso -2Baniso -3
1--1.216 Å2-0 Å20.871 Å2
2---1.658 Å20 Å2
3---1.265 Å2
Refinement stepCycle: LAST / Resolution: 1.66→67.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4141 0 80 622 4843
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0124668
X-RAY DIFFRACTIONr_bond_other_d0.0040.0164482
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.676384
X-RAY DIFFRACTIONr_angle_other_deg0.7371.5910440
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5415636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.737530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.80510918
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.63310226
X-RAY DIFFRACTIONr_chiral_restr0.1220.2729
X-RAY DIFFRACTIONr_chiral_restr_other2.3170.24
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025554
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021065
X-RAY DIFFRACTIONr_nbd_refined0.2010.2899
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1580.23935
X-RAY DIFFRACTIONr_nbtor_refined0.1660.22194
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.22529
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2498
X-RAY DIFFRACTIONr_metal_ion_refined0.1130.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.140.228
X-RAY DIFFRACTIONr_nbd_other0.140.2123
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2250.234
X-RAY DIFFRACTIONr_mcbond_it1.5891.8692222
X-RAY DIFFRACTIONr_mcbond_other1.5821.8672221
X-RAY DIFFRACTIONr_mcangle_it2.2993.3632806
X-RAY DIFFRACTIONr_mcangle_other2.33.3642807
X-RAY DIFFRACTIONr_scbond_it1.9842.0612446
X-RAY DIFFRACTIONr_scbond_other1.9832.0622447
X-RAY DIFFRACTIONr_scangle_it3.0593.7073519
X-RAY DIFFRACTIONr_scangle_other3.0593.7073520
X-RAY DIFFRACTIONr_lrange_it5.722.985541
X-RAY DIFFRACTIONr_lrange_other5.53321.055345
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
1.66-1.7030.2932140.25741920.25950900.9320.9586.56190.238
1.703-1.750.2792500.22845050.23150290.9410.95994.55160.208
1.75-1.80.2542010.20645280.20848480.9460.96697.54540.185
1.8-1.8560.2652090.19344830.19647320.950.97299.15470.176
1.856-1.9170.2252200.19843420.19945660.9620.9799.91240.181
1.917-1.9840.2412360.19141770.19344140.9590.97399.97730.175
1.984-2.0590.2222160.18340590.18542750.9640.9761000.171
2.059-2.1430.2461470.18539800.18741270.9560.9751000.174
2.143-2.2380.2362210.18437680.18639900.9610.97599.97490.174
2.238-2.3470.2541560.18935890.19237450.9610.9741000.181
2.347-2.4740.2181600.19134550.19236160.9660.97499.97230.184
2.474-2.6230.2121730.18132570.18234300.9730.9781000.178
2.623-2.8040.2691810.19230150.19631980.950.97599.93750.191
2.804-3.0290.2211420.18328440.18429890.9660.97699.89960.186
3.029-3.3170.2271200.18926420.19127620.9620.9741000.194
3.317-3.7070.2351190.19323600.19524810.9620.97599.91940.201
3.707-4.2790.1981400.19120710.19122170.9710.97499.72940.202
4.279-5.2350.211990.18217960.18319000.9750.97999.73680.197
5.235-7.3810.225910.20613850.20714760.9740.9741000.222
7.381-67.390.222270.1998130.28420.9730.9799.76250.221
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)
11.4661-0.25810.02110.539-0.12810.0331-0.03070.02030.2746-0.05540.0326-0.03680.0112-0.0152-0.00190.0609-0.0136-0.00440.03560.00150.05217.7901-4.870115.9306
22.01670.02060.15620.3632-0.00380.0340.03850.0454-0.24290.0157-0.0270.01010.0059-0.007-0.01150.05970.0169-0.0030.0271-0.01070.03171.57010.498350.8784
Refinement TLS groupSelection: ALL

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