PDB-8rsi: Crystal structure of Methanobrevibacter oralis macrodomain

ID or keywords:

Entry

Database: PDB / ID: 8rsi

Title

Crystal structure of Methanobrevibacter oralis macrodomain

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: 2.059 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

-
Download

PDBx/mmCIF format	8rsi.cif.gz	303.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8rsi.ent.gz	191.4 KB	Display	PDB format
PDBx/mmJSON format	8rsi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8rsi_validation.pdf.gz	478.2 KB	Display	wwPDB validaton report
Full document	8rsi_full_validation.pdf.gz	486 KB	Display
Data in XML	8rsi_validation.xml.gz	26.8 KB	Display
Data in CIF	8rsi_validation.cif.gz	35.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rs/8rsi ftp://data.pdbj.org/pub/pdb/validation_reports/rs/8rsi	HTTPS FTP

-
Related structure data

Related structure data	8rsjC 8rskC 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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#235 - Jul 2019 AMPA Receptor similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1)

Deposited unit

A: O-acetyl-ADP-ribose deacetylase

B: O-acetyl-ADP-ribose deacetylase

hetero molecules

60.4 kDa, 2 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
30.1 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
30.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	70.320, 146.609, 58.295
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: GLY / End label comp-ID: GLY / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 0 - 259 / Label seq-ID: 2 - 261

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Protein , 1 types, 2 molecules AB

#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

#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

-
Non-polymers , 5 types, 182 molecules

#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#5: Chemical	ChemComp-GLU / GLUTAMIC ACID Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₅H₉NO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	N
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.53 Å³/Da / Density % sol: 51.42 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 46.8 mM MES monohydrate, 53.2 mM imidazole, 20% (v/v) ethylene glycol, 10% (w/v) PEG8000

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.28229 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 13, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.28229 Å / Relative weight: 1
Reflection	Resolution: 2.059→146.39 Å / Num. obs: 38093 / % possible obs: 100 % / Redundancy: 12.1 % / CC_1/2: 0.992 / Net I/σ(I): 6.7
Reflection shell	Resolution: 2.059→2.11 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2762 / CC_1/2: 0.457

-
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: 2.059→73.412 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.937 / SU B: 13.071 / SU ML: 0.16 / Cross valid method: FREE R-VALUE / ESU R: 0.207 / ESU R Free: 0.183
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2437	1799	4.739 %
R_work	0.1927	36161	-
all	0.195	-	-
obs	-	37960	99.478 %

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: 45.758 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.076 Å²	-0 Å²	0 Å²
2-	-	1.585 Å²	-0 Å²
3-	-	-	-0.509 Å²

Refinement step

Cycle: LAST / Resolution: 2.059→73.412 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4124	0	60	169	4353

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	4559
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	4432
X-RAY DIFFRACTION	r_angle_refined_deg	1.729	1.652	6179
X-RAY DIFFRACTION	r_angle_other_deg	0.58	1.574	10298
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.413	5	607
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.77	5	30
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.11	10	908
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.447	10	227
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	692
X-RAY DIFFRACTION	r_chiral_restr_other	0.006	0.2	2
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	5387
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1041
X-RAY DIFFRACTION	r_nbd_refined	0.23	0.2	908
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.19	0.2	3786
X-RAY DIFFRACTION	r_nbtor_refined	0.187	0.2	2161
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	2640
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.181	0.2	169
X-RAY DIFFRACTION	r_metal_ion_refined	0.101	0.2	5
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.329	0.2	31
X-RAY DIFFRACTION	r_nbd_other	0.179	0.2	89
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.271	0.2	11
X-RAY DIFFRACTION	r_mcbond_it	3.008	2.965	2175
X-RAY DIFFRACTION	r_mcbond_other	3.007	2.966	2175
X-RAY DIFFRACTION	r_mcangle_it	4.373	5.311	2737
X-RAY DIFFRACTION	r_mcangle_other	4.372	5.312	2738
X-RAY DIFFRACTION	r_scbond_it	4.227	3.444	2384
X-RAY DIFFRACTION	r_scbond_other	4.167	3.444	2383
X-RAY DIFFRACTION	r_scangle_it	6.243	6.132	3395
X-RAY DIFFRACTION	r_scangle_other	6.243	6.133	3396
X-RAY DIFFRACTION	r_lrange_it	8.276	29.206	5061
X-RAY DIFFRACTION	r_lrange_other	8.275	29.166	5041
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.091	0.05	8669

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	0.09139	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.09139	0.05009

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
2.059-2.112	0.373	125	0.341	2528	0.342	2757	0.893	0.902	96.2278	0.344
2.112-2.17	0.306	123	0.296	2587	0.297	2711	0.924	0.93	99.9631	0.297
2.17-2.233	0.318	122	0.269	2538	0.271	2660	0.927	0.941	100	0.27
2.233-2.301	0.248	137	0.253	2379	0.252	2516	0.951	0.95	100	0.25
2.301-2.377	0.312	116	0.229	2370	0.232	2486	0.924	0.96	100	0.223
2.377-2.46	0.251	106	0.223	2316	0.225	2422	0.955	0.968	100	0.217
2.46-2.553	0.3	95	0.213	2223	0.217	2318	0.939	0.972	100	0.202
2.553-2.657	0.279	101	0.208	2151	0.212	2252	0.957	0.975	100	0.193
2.657-2.775	0.262	85	0.191	2090	0.194	2176	0.971	0.979	99.954	0.177
2.775-2.91	0.271	106	0.176	1936	0.18	2046	0.954	0.982	99.8045	0.161
2.91-3.067	0.252	102	0.161	1867	0.165	1972	0.967	0.984	99.8479	0.147
3.067-3.253	0.245	83	0.166	1788	0.169	1878	0.96	0.984	99.6273	0.158
3.253-3.477	0.201	75	0.164	1656	0.166	1741	0.975	0.986	99.4256	0.16
3.477-3.755	0.248	77	0.182	1562	0.185	1649	0.964	0.984	99.3936	0.184
3.755-4.113	0.23	56	0.176	1454	0.178	1532	0.97	0.984	98.564	0.182
4.113-4.596	0.16	81	0.134	1286	0.136	1380	0.986	0.99	99.058	0.148
4.596-5.304	0.173	75	0.14	1152	0.142	1243	0.985	0.99	98.7128	0.158
5.304-6.487	0.305	58	0.213	998	0.218	1062	0.959	0.977	99.435	0.234
6.487-9.139	0.211	55	0.18	787	0.182	844	0.976	0.982	99.763	0.212
9.139-73.412	0.303	21	0.219	493	0.222	514	0.959	0.967	100	0.272

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	2.8899	0.326	-0.6425	0.7745	-0.4936	0.6737	-0.0863	0.0331	-0.6003	-0.0164	-0.0723	-0.082	0.0442	0.0622	0.1586	0.0089	-0.0162	0.028	0.0783	-0.0368	0.142	-11.982	19.949	-20.4122
2	0.6772	0.011	0.0177	1.6938	0.255	2.7077	-0.0429	-0.0174	-0.045	0.0553	0.1556	0.225	0.1606	-0.3377	-0.1127	0.0153	-0.0296	0.0066	0.1811	0.0056	0.052	-40.7428	22.4639	-11.9521
3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.0503	0	0	0.0503	0	0.0503	0	0	0

Refinement TLS group

Selection: ALL

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 5 types, 182 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 1 types, 2 molecules AB

-Non-polymers , 5 types, 182 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 5 types, 182 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi