PDB-3bpq: Crystal Structure of RelB-RelE antitoxin-toxin complex from Metha...

ID or keywords:

Entry

Database: PDB / ID: 3bpq

Title

Crystal Structure of RelB-RelE antitoxin-toxin complex from Methanococcus jannaschii

Components

Antitoxin RelB3
Toxin RelE3

Keywords

TOXIN / protein toxin-antitoxin complex

Function / homology

Function and homology information

nuclease activity /

Hydrolases; Acting on ester bonds
Similarity search - Function

Biological species

Methanocaldococcus jannaschii (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MIR / Resolution: 2.2 Å

Authors

Francuski, D. / Saenger, W.

Citation

Journal: J.Mol.Biol. / Year: 2009
Title: Crystal structure of the antitoxin-toxin protein complex RelB-RelE from Methanococcus jannaschii
Authors: Francuski, D. / Saenger, W.

History

Deposition	Dec 19, 2007	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Dec 23, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Aug 24, 2011	Group: Database references / Source and taxonomy
Revision 1.3	Aug 31, 2011	Group: Database references / Structure summary
Revision 1.4	Oct 25, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.5	Mar 13, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3bpq.cif.gz	64.4 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bp/3bpq ftp://data.pdbj.org/pub/pdb/validation_reports/bp/3bpq	HTTPS FTP

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Related structure data

Similar structure data	5fk0-8 5fk0-5 5fjw-1 5fk0-4 5fk0-1 5fjw-8 5fk0-6 5xfh-d 5o0q-4 5o0m-1 Search similar-shape structures by Omokage search (details) 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: Antitoxin RelB3

B: Toxin RelE3

C: Antitoxin RelB3

D: Toxin RelE3

33.7 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	52.794, 57.992, 58.747
Angle α, β, γ (deg.)	90.00, 92.30, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Antitoxin RelB3 / RelB Mass: 6323.375 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Strain: DSM2661 / Gene: relB3, relB, MJ1103.1 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / References: UniProt: P0CL56
#2: Protein	Toxin RelE3 / Uncharacterized protein MJ1103 / MjRelE / Putative endoribonuclease RelE Mass: 10515.409 Da / Num. of mol.: 2 / Mutation: R62S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Strain: DSM2661 / Gene: MJ1103, relE, relE3 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 References: UniProt: Q58503, Hydrolases; Acting on ester bonds
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.67 Å³/Da / Density % sol: 53.9 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 20%MPD, 0.1M Bis-Tris pH5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.94905 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 12, 2006 / Details: mirrors
Radiation	Monochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.94905 Å / Relative weight: 1
Reflection	Resolution: 2.13→50 Å / Num. obs: 19952 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 4.2 % / R_merge(I) obs: 0.05 / Net I/σ(I): 15.4
Reflection shell	Resolution: 2.13→2.18 Å / Redundancy: 4.1 % / R_merge(I) obs: 0.421 / Mean I/σ(I) obs: 3.13 / Num. unique all: 1332 / % possible all: 98.9

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Phasing

Phasing

Method:

MIR

Phasing set

ID
1
2
3

Phasing MIR der

Native set-ID: 1 / Resolution: 2.13→32.95 Å

ID	R cullis acentric	R cullis centric	Der set-ID	Reflection acentric	Reflection centric
ISO_1	0	0	1	18691	951
ISO_2	0.842	0.794	2	10255	302
ISO_3	0.907	0.792	3	8870	271

Phasing MIR der shell

Highest resolution (Å)	Lowest resolution (Å)	Der-ID	R cullis acentric	R cullis centric	Reflection acentric	Reflection centric
9.17	32.95	ISO_1	0	0	166	36
6.61	9.17	ISO_1	0	0	372	46
5.44	6.61	ISO_1	0	0	491	56
4.72	5.44	ISO_1	0	0	589	53
4.23	4.72	ISO_1	0	0	656	47
3.87	4.23	ISO_1	0	0	725	46
3.59	3.87	ISO_1	0	0	797	41
3.36	3.59	ISO_1	0	0	864	34
3.17	3.36	ISO_1	0	0	904	45
3.01	3.17	ISO_1	0	0	963	43
2.87	3.01	ISO_1	0	0	1015	49
2.75	2.87	ISO_1	0	0	1060	50
2.64	2.75	ISO_1	0	0	1109	44
2.54	2.64	ISO_1	0	0	1140	51
2.46	2.54	ISO_1	0	0	1223	51
2.38	2.46	ISO_1	0	0	1238	54
2.31	2.38	ISO_1	0	0	1276	51
2.24	2.31	ISO_1	0	0	1325	57
2.19	2.24	ISO_1	0	0	1377	54
2.13	2.19	ISO_1	0	0	1401	43
9.17	32.95	ISO_2	0.673	0.732	165	18
6.61	9.17	ISO_2	0.74	0.712	372	21
5.44	6.61	ISO_2	0.778	0.724	491	30
4.72	5.44	ISO_2	0.803	0.875	589	25
4.23	4.72	ISO_2	0.872	0.8	656	26
3.87	4.23	ISO_2	0.903	0.765	725	20
3.59	3.87	ISO_2	0.887	0.803	795	19
3.36	3.59	ISO_2	0.876	0.921	864	15
3.17	3.36	ISO_2	0.873	1.005	904	22
3.01	3.17	ISO_2	0.903	0.845	962	24
2.87	3.01	ISO_2	0.902	0.966	1014	24
2.75	2.87	ISO_2	0.885	1.169	1059	23
2.64	2.75	ISO_2	0.942	1.002	1108	25
2.54	2.64	ISO_2	0.967	1.658	551	10
2.46	2.54	ISO_2	0	0	0	0
2.38	2.46	ISO_2	0	0	0	0
2.31	2.38	ISO_2	0	0	0	0
2.24	2.31	ISO_2	0	0	0	0
2.19	2.24	ISO_2	0	0	0	0
2.13	2.19	ISO_2	0	0	0	0
9.17	32.95	ISO_3	0.759	0.637	165	18
6.61	9.17	ISO_3	0.821	0.931	372	22
5.44	6.61	ISO_3	0.843	0.869	491	30
4.72	5.44	ISO_3	0.932	0.906	588	25
4.23	4.72	ISO_3	0.94	0.757	653	26
3.87	4.23	ISO_3	0.95	1.039	725	21
3.59	3.87	ISO_3	0.942	0.902	797	19
3.36	3.59	ISO_3	0.954	0.877	864	16
3.17	3.36	ISO_3	0.974	0.95	902	21
3.01	3.17	ISO_3	1.002	1.371	961	24
2.87	3.01	ISO_3	0.993	0.844	1014	24
2.75	2.87	ISO_3	1.042	1.099	1046	22
2.64	2.75	ISO_3	1.025	0.775	292	3
2.54	2.64	ISO_3	0	0	0	0
2.46	2.54	ISO_3	0	0	0	0
2.38	2.46	ISO_3	0	0	0	0
2.31	2.38	ISO_3	0	0	0	0
2.24	2.31	ISO_3	0	0	0	0
2.19	2.24	ISO_3	0	0	0	0
2.13	2.19	ISO_3	0	0	0	0

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
MAR345		data collection
HKL-2000		data reduction
SCALEPACK		data scaling
SHARP		phasing

Refinement

Method to determine structure:

MIR / Resolution: 2.2→20 Å / Cor.coef. F_o:F_c: 0.939 / Cor.coef. F_o:F_c free: 0.903 / SU B: 16.068 / SU ML: 0.202 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.273 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27418	931	5.1 %	RANDOM
R_work	0.23825	-	-	-
obs	0.24007	17159	99.71 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 50.042 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.73 Å²	0 Å²	3.78 Å²
2-	-	-3.96 Å²	0 Å²
3-	-	-	3.53 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2118	0	0	56	2174

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	2173
X-RAY DIFFRACTION	r_angle_refined_deg	1.058	1.977	2908
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.217	5	252
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.571	23.704	108
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.5	15	452
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.487	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	318
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	1584
X-RAY DIFFRACTION	r_nbd_refined	0.198	0.2	909
X-RAY DIFFRACTION	r_nbtor_refined	0.304	0.2	1446
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.131	0.2	96
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.161	0.2	16
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.094	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	0.388	1.5	1310
X-RAY DIFFRACTION	r_mcangle_it	0.661	2	2039
X-RAY DIFFRACTION	r_scbond_it	0.961	3	980
X-RAY DIFFRACTION	r_scangle_it	1.403	4.5	866

LS refinement shell

Resolution: 2.2→2.256 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.296	70	-
R_work	0.268	1242	-
obs	-	-	100 %

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	8.8929	2.5767	-6.6565	7.3312	-5.45	11.307	0.6249	0.536	0.2607	0.5088	-0.19	0.296	-0.8216	0.1877	-0.4348	-0.1667	0.008	-0.0289	-0.1954	-0.0559	-0.0188	-2.299	39.966	23.113
2	6.4152	1.5309	-1.5602	7.8828	-0.277	5.324	0.0078	0.377	0.0736	0.1306	-0.007	0.9151	-0.0205	-0.3079	-0.0009	-0.1992	0.025	-0.0023	-0.2159	-0.0205	-0.0205	-9.319	41.505	26.466
3	10.3537	-12.1209	-8.9644	20.4175	12.7056	11.2747	0.4176	0.2688	0.538	-0.8323	0.0404	-0.7986	-0.5259	-0.201	-0.4579	-0.2091	-0.0402	0.0383	-0.0279	-0.019	-0.1145	16.676	33.295	10.017
4	5.0598	0.1154	-0.4111	8.8884	1.2509	6.3362	0.0442	0.1027	0.2956	-0.4003	0.1466	-0.464	-0.0105	0.1377	-0.1908	-0.2008	-0.0423	0.0602	0.0047	-0.0787	-0.1166	23.549	32.221	6.211

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	8 - 48	8 - 48
2	X-RAY DIFFRACTION	2	B	B	3 - 88	3 - 88
3	X-RAY DIFFRACTION	3	C	C	9 - 47	9 - 47
4	X-RAY DIFFRACTION	4	D	D	3 - 88	3 - 88

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