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

ID or keywords:

Entry

Database: PDB / ID: 8rsk

Title

Crystal structure of Methanobrevibacter oralis macrodomain in complex with Asn-ADPr

Components

O-acetyl-ADP-ribose deacetylase

Keywords

HYDROLASE / 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

Biological species

Methanobrevibacter oralis (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.359 Å

Authors

Ariza, A.

Funding support

United Kingdom, 4items

Organization	Grant number	Country
Wellcome Trust	210634	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

Citation

Journal: 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

Deposition	Jan 24, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 25, 2024	Provider: repository / Type: Initial release
Revision 1.1	Oct 2, 2024	Group: 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 1.2	Oct 16, 2024	Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details Item: _citation.journal_volume / _citation_author.name / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8rsk.cif.gz	442.9 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	8rsk_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	8rsk_full_validation.pdf.gz	1.3 MB	Display
Data in XML	8rsk_validation.xml.gz	39.1 KB	Display
Data in CIF	8rsk_validation.cif.gz	49.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rs/8rsk ftp://data.pdbj.org/pub/pdb/validation_reports/rs/8rsk	HTTPS FTP

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Related structure data

Related structure data	8rsiC 8rsjC 8rslC 8rsmC 8rsnC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: O-acetyl-ADP-ribose deacetylase

B: O-acetyl-ADP-ribose deacetylase

C: O-acetyl-ADP-ribose deacetylase

hetero molecules

92.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: O-acetyl-ADP-ribose deacetylase

hetero molecules

defined by author
Evidence: gel filtration
30.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: O-acetyl-ADP-ribose deacetylase

hetero molecules

defined by author
30.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: O-acetyl-ADP-ribose deacetylase

hetero molecules

defined by author
30.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	104.146, 110.443, 104.610
Angle α, β, γ (deg.)	90.000, 119.559, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-302- ZN
2	1	B-304- ZN
3	1	C-302- ZN

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A

NCS domain segments:

Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ASN / End label comp-ID: ASN / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: -1 - 260 / Label seq-ID: 1 - 262

Dom-ID	Component-ID	Ens-ID
1	1	1
2	1	1
3	2	2
4	2	2
5	3	3
6	3	3

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6

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Protein , 1 types, 3 molecules ABC

#1: Protein	O-acetyl-ADP-ribose deacetylase / Methonobrevibacter oralis macrodomain Mass: 29671.775 Da / Num. of mol.: 3 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

#1: Protein

O-acetyl-ADP-ribose deacetylase / Methonobrevibacter oralis macrodomain

Mass: 29671.775 Da / Num. of mol.: 3
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

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Non-polymers , 5 types, 194 molecules

#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-A1H20 / (2~{S})-4-[[(2~{S},3~{R},4~{S},5~{R})-5-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]amino]-2-azanyl-4-oxidanylidene-butanoic acid Mass: 673.418 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₉H₂₉N₇O₁₆P₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.94 Å³/Da / Density % sol: 58.16 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 5 mM zinc acetate, 9% (w/v) PEG8000, 100 mM sodium cocadylate pH 6.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.92819 Å / Relative weight: 1
Reflection	Resolution: 2.359→69.955 Å / Num. obs: 42263 / % possible obs: 99.9 % / Redundancy: 3.1 % / CC_1/2: 0.993 / Net I/σ(I): 7.3
Reflection shell	Resolution: 2.36→2.42 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3109 / CC_1/2: 0.494

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0415	refinement
DIALS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.359→69.955 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.929 / SU B: 26.387 / SU ML: 0.265 / Cross valid method: FREE R-VALUE / ESU R: 0.36 / ESU R Free: 0.255
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2607	1951	4.64 %
R_work	0.2134	40100	-
all	0.216	-	-
obs	-	42051	99.151 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 58.761 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.475 Å²	-0 Å²	0.736 Å²
2-	-	-3.208 Å²	-0 Å²
3-	-	-	1.156 Å²

Refinement step

Cycle: LAST / Resolution: 2.359→69.955 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6225	0	185	174	6584

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.012	6609
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	6212
X-RAY DIFFRACTION	r_angle_refined_deg	2.211	1.678	8910
X-RAY DIFFRACTION	r_angle_other_deg	0.683	1.592	14355
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.431	5	807
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	10.207	5	36
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.358	10	1205
X-RAY DIFFRACTION	r_dihedral_angle_other_3_deg	16.985	10	6
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.049	10	313
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	1013
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	7620
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1476
X-RAY DIFFRACTION	r_nbd_refined	0.227	0.2	1172
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.197	0.2	5264
X-RAY DIFFRACTION	r_nbtor_refined	0.182	0.2	3101
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	3744
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.16	0.2	137
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.014	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.218	0.2	28
X-RAY DIFFRACTION	r_nbd_other	0.45	0.2	62
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.291	0.2	10
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.098	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	2.927	2.312	3176
X-RAY DIFFRACTION	r_mcbond_other	2.893	2.31	3173
X-RAY DIFFRACTION	r_mcangle_it	4.577	4.148	3963
X-RAY DIFFRACTION	r_mcangle_other	4.577	4.148	3964
X-RAY DIFFRACTION	r_scbond_it	3.945	2.625	3433
X-RAY DIFFRACTION	r_scbond_other	3.948	2.628	3434
X-RAY DIFFRACTION	r_scangle_it	5.758	4.642	4935
X-RAY DIFFRACTION	r_scangle_other	5.758	4.643	4936
X-RAY DIFFRACTION	r_lrange_it	8.483	22.308	6916
X-RAY DIFFRACTION	r_lrange_other	8.491	22.054	6903
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.091	0.05	7954
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.093	0.05	7928
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.095	0.05	7944

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.09092	0.05008
1	2	A	X-RAY DIFFRACTION	Local ncs	0.09092	0.05008
2	3	A	X-RAY DIFFRACTION	Local ncs	0.09252	0.05008
2	4	A	X-RAY DIFFRACTION	Local ncs	0.09252	0.05008
3	5	A	X-RAY DIFFRACTION	Local ncs	0.09451	0.05008
3	6	A	X-RAY DIFFRACTION	Local ncs	0.09451	0.05008

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.359-2.42	0.394	159	0.382	2839	0.383	3115	0.889	0.904	96.244	0.379
2.42-2.487	0.39	135	0.362	2862	0.363	3045	0.908	0.915	98.4236	0.363
2.487-2.559	0.386	129	0.344	2785	0.346	2944	0.907	0.932	98.981	0.339
2.559-2.637	0.353	144	0.317	2687	0.318	2863	0.932	0.944	98.8823	0.306
2.637-2.724	0.371	144	0.307	2635	0.31	2800	0.921	0.949	99.25	0.29
2.724-2.819	0.347	133	0.284	2573	0.287	2725	0.936	0.958	99.3027	0.255
2.819-2.925	0.323	129	0.262	2453	0.266	2593	0.935	0.962	99.5758	0.234
2.925-3.044	0.284	124	0.23	2386	0.233	2517	0.96	0.972	99.7219	0.203
3.044-3.18	0.36	105	0.231	2284	0.236	2399	0.923	0.972	99.5832	0.206
3.18-3.334	0.25	110	0.217	2158	0.219	2278	0.964	0.978	99.561	0.2
3.334-3.514	0.281	88	0.212	2089	0.215	2185	0.962	0.979	99.6339	0.198
3.514-3.727	0.304	81	0.221	2005	0.225	2089	0.956	0.978	99.8564	0.208
3.727-3.983	0.245	73	0.184	1871	0.186	1950	0.971	0.986	99.6923	0.172
3.983-4.301	0.188	71	0.159	1723	0.161	1800	0.98	0.986	99.6667	0.145
4.301-4.71	0.203	81	0.144	1606	0.147	1692	0.976	0.989	99.7045	0.132
4.71-5.263	0.157	55	0.139	1466	0.139	1522	0.987	0.992	99.9343	0.129
5.263-6.072	0.218	52	0.153	1272	0.156	1332	0.98	0.989	99.3994	0.142
6.072-7.422	0.196	48	0.145	1101	0.147	1152	0.982	0.99	99.7396	0.138
7.422-10.438	0.143	54	0.12	838	0.122	895	0.987	0.992	99.6648	0.114
10.438-69.955	0.171	36	0.209	467	0.207	513	0.982	0.968	98.0507	0.28

Refinement TLS params.

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

ID	L11 (°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)
1	5.5887	-0.0304	1.9927	1.3443	0.443	2.4748	-0.0673	-0.0535	0.604	-0.122	-0.1005	0.086	-0.0321	-0.1734	0.1678	0.0369	-0.0259	0.0231	0.4957	-0.0272	0.143	58.8244	-8.1579	35.2354
2	2.277	-0.3346	0.948	1.2406	0.2774	6.1278	-0.0895	0.0284	0.0969	-0.1939	-0.0614	-0.0207	-0.737	-0.4236	0.1509	0.1103	0.0437	-0.0139	0.4094	-0.0521	0.0119	24.9389	-8.8706	23.3593
3	3.5568	-0.1395	-0.1513	2.1656	0.1875	2.9231	-0.0591	-0.5255	-0.0557	0.1028	0.0916	0.1188	-0.2339	-0.1957	-0.0326	0.0525	0.0142	0.0492	0.5481	0.0175	0.068	86.3738	-9.2866	12.06

Refinement TLS group

Selection: ALL

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