PDB-8rsl: Crystal structure of Staphylococcus aureus macrodomain

ID or keywords:

Entry

Database: PDB / ID: 8rsl

Title

Crystal structure of Staphylococcus aureus macrodomain

Components

Protein-ADP-ribose hydrolase

Keywords

HYDROLASE / ADP-RIBOSYLATION / ADP-RIBOSE / ADP-RIBOSYLHYDROLASE / Lipoylation / Metalloenzyme

Function / homology

hydrolase activity, acting on glycosyl bonds / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / Protein-ADP-ribose hydrolase

Function and homology information

Biological species

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.94 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	8rsl.cif.gz	303.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8rsl.ent.gz	188.7 KB	Display	PDB format
PDBx/mmJSON format	8rsl.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8rsl_validation.pdf.gz	439.4 KB	Display	wwPDB validaton report
Full document	8rsl_full_validation.pdf.gz	443.9 KB	Display
Data in XML	8rsl_validation.xml.gz	28.3 KB	Display
Data in CIF	8rsl_validation.cif.gz	39.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rs/8rsl ftp://data.pdbj.org/pub/pdb/validation_reports/rs/8rsl	HTTPS FTP

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Related structure data

Related structure data	8rsiC 8rsjC 8rskC 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: Protein-ADP-ribose hydrolase

B: Protein-ADP-ribose hydrolase

hetero molecules

65.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Protein-ADP-ribose hydrolase

hetero molecules

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

2

B: Protein-ADP-ribose hydrolase

hetero molecules

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

Unit cell

Length a, b, c (Å)	40.190, 139.400, 49.190
Angle α, β, γ (deg.)	90.000, 93.760, 90.000
Int Tables number	4
Space group name H-M	P12₁1

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: ARG / Beg label comp-ID: ARG / End auth comp-ID: ASP / End label comp-ID: ASP / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: -6 - 264 / Label seq-ID: 17 - 287

Dom-ID
1
2

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

#1: Protein	Protein-ADP-ribose hydrolase Mass: 32610.221 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) Gene: ymdB, G6X24_05250, G6Y24_06505, GO793_03185, GO829_13425, GO941_07705, M1K003_0429, SAMEA70153168_00686 Production host: Escherichia coli (E. coli) / References: UniProt: A0A390ZNG0
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 2.11 Å³/Da / Density % sol: 41.66 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 18.5% (v/v) PEG400, 12.5% (v/v) 1-propanol, 4% (v/v) glycerol

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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: 0.92 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 19, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.92 Å / Relative weight: 1
Reflection	Resolution: 1.94→49.084 Å / Num. obs: 39007 / % possible obs: 97.9 % / Redundancy: 3.4 % / CC_1/2: 0.999 / Net I/σ(I): 18.8
Reflection shell	Resolution: 1.94→1.99 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2881 / CC_1/2: 0.702

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0415	refinement
xia2		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.94→49.084 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.941 / SU B: 7.223 / SU ML: 0.105 / Cross valid method: FREE R-VALUE / ESU R: 0.165 / ESU R Free: 0.151
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2132	1911	4.903 %
R_work	0.1635	37063	-
all	0.166	-	-
obs	-	38974	97.772 %

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: 33.165 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.806 Å²	-0 Å²	-0.056 Å²
2-	-	0.14 Å²	0 Å²
3-	-	-	0.668 Å²

Refinement step

Cycle: LAST / Resolution: 1.94→49.084 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4282	0	2	346	4630

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	4467
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	4314
X-RAY DIFFRACTION	r_angle_refined_deg	1.699	1.651	6070
X-RAY DIFFRACTION	r_angle_other_deg	0.596	1.583	9937
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.277	5	580
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.48	5	30
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.923	10	822
X-RAY DIFFRACTION	r_dihedral_angle_other_3_deg	17.169	10	4
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.585	10	216
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	697
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	5318
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1017
X-RAY DIFFRACTION	r_nbd_refined	0.221	0.2	857
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.183	0.2	3722
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	2174
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	2541
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.175	0.2	265
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.095	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.293	0.2	35
X-RAY DIFFRACTION	r_nbd_other	0.23	0.2	110
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.189	0.2	17
X-RAY DIFFRACTION	r_mcbond_it	3.359	2.447	2206
X-RAY DIFFRACTION	r_mcbond_other	3.349	2.447	2206
X-RAY DIFFRACTION	r_mcangle_it	4.808	4.375	2764
X-RAY DIFFRACTION	r_mcangle_other	4.808	4.376	2765
X-RAY DIFFRACTION	r_scbond_it	4.461	3.003	2261
X-RAY DIFFRACTION	r_scbond_other	4.462	3.002	2260
X-RAY DIFFRACTION	r_scangle_it	6.802	5.2	3286
X-RAY DIFFRACTION	r_scangle_other	6.801	5.201	3287
X-RAY DIFFRACTION	r_lrange_it	8.945	29.88	5031
X-RAY DIFFRACTION	r_lrange_other	8.917	28.974	4970
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.08	0.05	8749

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	0.07988	0.05008
1	2	A	X-RAY DIFFRACTION	Local ncs	0.07988	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
1.94-1.99	0.301	125	0.258	2748	0.26	2975	0.953	0.96	96.5714	0.246
1.99-2.045	0.284	121	0.221	2670	0.224	2839	0.957	0.97	98.3093	0.205
2.045-2.104	0.25	124	0.187	2612	0.19	2779	0.962	0.977	98.4527	0.167
2.104-2.169	0.199	131	0.172	2531	0.173	2693	0.978	0.982	98.8489	0.152
2.169-2.24	0.225	145	0.162	2467	0.166	2656	0.967	0.984	98.3434	0.142
2.24-2.318	0.211	118	0.157	2348	0.16	2500	0.97	0.985	98.64	0.138
2.318-2.405	0.218	114	0.15	2280	0.153	2432	0.972	0.987	98.4375	0.13
2.405-2.503	0.247	107	0.15	2185	0.154	2388	0.968	0.987	95.9799	0.129
2.503-2.614	0.188	98	0.142	2137	0.145	2248	0.979	0.988	99.4217	0.124
2.614-2.741	0.231	100	0.151	2061	0.154	2176	0.97	0.986	99.3107	0.132
2.741-2.889	0.224	108	0.163	1942	0.167	2065	0.966	0.984	99.2736	0.147
2.889-3.064	0.221	97	0.161	1812	0.164	1937	0.974	0.985	98.5545	0.146
3.064-3.274	0.234	104	0.17	1685	0.173	1845	0.963	0.984	96.9648	0.158
3.274-3.536	0.215	84	0.17	1529	0.172	1691	0.976	0.985	95.3873	0.162
3.536-3.871	0.184	98	0.162	1410	0.164	1575	0.981	0.986	95.746	0.158
3.871-4.325	0.207	65	0.137	1318	0.14	1413	0.976	0.989	97.8769	0.135
4.325-4.987	0.16	56	0.135	1167	0.136	1274	0.987	0.99	95.9969	0.135
4.987-6.092	0.268	55	0.175	983	0.18	1066	0.959	0.987	97.3734	0.175
6.092-8.55	0.196	45	0.18	735	0.181	830	0.975	0.983	93.9759	0.184
8.55-49.084	0.146	16	0.183	443	0.181	479	0.989	0.983	95.8246	0.194

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	0.8587	-0.4173	-0.1378	1.4857	-0.1922	0.7678	-0.0176	0.032	0.0357	-0.1645	0.0368	0.0188	-0.0521	0.0286	-0.0192	0.04	-0.027	-0.0052	0.0449	0.0036	0.0026	58.8334	6.6709	21.4767
2	0.4742	0.4892	-0.0821	1.832	-0.382	0.8213	-0.0164	0.038	-0.0427	0.1665	0.0721	-0.0394	0.0505	0.0779	-0.0557	0.041	0.028	-0.0016	0.0557	-0.0001	0.0119	41.9421	-25.7897	3.9347

Refinement TLS group

Selection: ALL

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