PDB-2w82: The structure of ArdA

ID or keywords:

Entry

Database: PDB / ID: 2w82

Title

The structure of ArdA

Components

ORF18

Keywords

REPLICATION INHIBITOR / DNA MIMIC

Function / homology

Function and homology information

identical protein binding
Similarity search - Function

Biological species

ENTEROCOCCUS FAECALIS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SIRAS / Resolution: 2.8 Å

Authors

McMahon, S.A. / Roberts, G.A. / Carter, L.G. / Cooper, L.P. / Liu, H. / White, J.H. / Johnson, K.A. / Sanghvi, B. / Oke, M. / Walkinshaw, M.D. ...

Citation

Journal: Nucleic Acids Res. / Year: 2009
Title: Extensive DNA Mimicry by the Arda Anti-Restriction Protein and its Role in the Spread of Antibiotic Resistance.
Authors: Mcmahon, S.A. / Roberts, G.A. / Johnson, K.A. / Cooper, L.P. / Liu, H. / White, J.H. / Carter, L.G. / Sanghvi, B. / Oke, M. / Walkinshaw, M.D. / Blakely, G. / Naismith, J.H. / Dryden, D.T.F.

History

Deposition	Jan 8, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 27, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Aug 30, 2017	Group: Data collection / Category: diffrn_detector / reflns / reflns_shell Item: _diffrn_detector.type / _reflns.d_resolution_low ..._diffrn_detector.type / _reflns.d_resolution_low / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_redundancy / _reflns.percent_possible_obs / _reflns_shell.Rmerge_I_obs / _reflns_shell.percent_possible_all
Revision 1.3	May 8, 2024	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	2w82_validation.pdf.gz	444.7 KB	Display	wwPDB validaton report
Full document	2w82_full_validation.pdf.gz	448.1 KB	Display
Data in XML	2w82_validation.xml.gz	22.9 KB	Display
Data in CIF	2w82_validation.cif.gz	31.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w8/2w82 ftp://data.pdbj.org/pub/pdb/validation_reports/w8/2w82	HTTPS FTP

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Related structure data

Similar structure data	6poo-d 6ek4-4 6ek4-3 6fia-2 6e8f-3 5fmv-2 5fmv-1 3gng-d 6gy7-2 3gf5-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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: ORF18

B: ORF18

C: ORF18

D: ORF18

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

1

A: ORF18

B: ORF18

defined by author&software
38.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: ORF18

D: ORF18

defined by author&software
38.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	63.810, 103.440, 172.980
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Refine code: 5

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	GLN	GLN	ILE	ILE	A	A	5 - 37	5 - 37
2	1	1	GLN	GLN	ILE	ILE	C	C	5 - 37	5 - 37
1	2	1	TYR	TYR	ARG	ARG	A	A	46 - 68	46 - 68
2	2	1	TYR	TYR	ARG	ARG	C	C	46 - 68	46 - 68
1	1	2	LEU	LEU	ASP	ASP	A	A	69 - 103	69 - 103
2	1	2	LEU	LEU	ASP	ASP	C	C	69 - 103	69 - 103
1	1	3	ILE	ILE	VAL	VAL	A	A	104 - 164	104 - 164
2	1	3	ILE	ILE	VAL	VAL	C	C	104 - 164	104 - 164
1	1	4	GLN	GLN	GLY	GLY	B	B	5 - 12	5 - 12
2	1	4	GLN	GLN	GLY	GLY	D	D	5 - 12	5 - 12
1	2	4	GLY	GLY	ARG	ARG	B	B	21 - 68	21 - 68
2	2	4	GLY	GLY	ARG	ARG	D	D	21 - 68	21 - 68
1	1	5	LEU	LEU	ASP	ASP	B	B	69 - 103	69 - 103
2	1	5	LEU	LEU	ASP	ASP	D	D	69 - 103	69 - 103
1	1	6	ILE	ILE	VAL	VAL	B	B	104 - 164	104 - 164
2	1	6	ILE	ILE	VAL	VAL	D	D	104 - 164	104 - 164
1	1	7	GLN	GLN	GLY	GLY	A	A	5 - 12	5 - 12
2	1	7	GLN	GLN	GLY	GLY	B	B	5 - 12	5 - 12
3	1	7	GLN	GLN	GLY	GLY	D	D	5 - 12	5 - 12
1	2	7	GLY	GLY	ILE	ILE	A	A	21 - 37	21 - 37
2	2	7	GLY	GLY	ILE	ILE	B	B	21 - 37	21 - 37
3	2	7	GLY	GLY	ILE	ILE	D	D	21 - 37	21 - 37
1	3	7	TYR	TYR	ARG	ARG	A	A	46 - 68	46 - 68
2	3	7	TYR	TYR	ARG	ARG	B	B	46 - 68	46 - 68
3	3	7	TYR	TYR	ARG	ARG	D	D	46 - 68	46 - 68
1	1	8	LEU	LEU	ASP	ASP	A	A	69 - 103	69 - 103
2	1	8	LEU	LEU	ASP	ASP	B	B	69 - 103	69 - 103
3	1	8	LEU	LEU	ASP	ASP	D	D	69 - 103	69 - 103
1	1	9	ILE	ILE	GLY	GLY	A	A	104 - 128	104 - 128
2	1	9	ILE	ILE	GLY	GLY	B	B	104 - 128	104 - 128
3	1	9	ILE	ILE	GLY	GLY	D	D	104 - 128	104 - 128
1	2	9	ASP	ASP	VAL	VAL	A	A	139 - 164	139 - 164
2	2	9	ASP	ASP	VAL	VAL	B	B	139 - 164	139 - 164
3	2	9	ASP	ASP	VAL	VAL	D	D	139 - 164	139 - 164

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9

#1: Protein	ORF18 / ARDA Mass: 19135.883 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ENTEROCOCCUS FAECALIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q47730
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 51 / 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: 3.8 Å³/Da / Density % sol: 67.4 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.239
Detector	Type: ADSC / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.239 Å / Relative weight: 1
Reflection	Resolution: 2.8→12.5 Å / Num. obs: 27101 / % possible obs: 93.3 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / R_merge(I) obs: 0.064 / Net I/σ(I): 12.6
Reflection shell	Resolution: 2.8→2.87 Å / Redundancy: 2.5 % / R_merge(I) obs: 0.565 / Mean I/σ(I) obs: 1.8 / % possible all: 93.6

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

SIRAS
Starting model: NONE

Resolution: 2.8→29.44 Å / Cor.coef. F_o:F_c: 0.933 / Cor.coef. F_o:F_c free: 0.899 / SU B: 26.186 / SU ML: 0.242 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.675 / ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.249	1377	5.1 %	RANDOM
R_work	0.207	-	-	-
obs	0.209	25724	93.5 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 43.72 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.34 Å²	0 Å²	0 Å²
2-	-	0.19 Å²	0 Å²
3-	-	-	0.15 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→29.44 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5310	0	0	51	5361

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.022	5436
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3464
X-RAY DIFFRACTION	r_angle_refined_deg	0.817	1.953	7392
X-RAY DIFFRACTION	r_angle_other_deg	0.762	3	8472
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.585	5	646
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.644	25.806	310
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.714	15	882
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.8	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.051	0.2	790
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	6170
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1098
X-RAY DIFFRACTION	r_nbd_refined	0.184	0.2	949
X-RAY DIFFRACTION	r_nbd_other	0.162	0.2	3334
X-RAY DIFFRACTION	r_nbtor_refined	0.179	0.2	2662
X-RAY DIFFRACTION	r_nbtor_other	0.08	0.2	2726
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.119	0.2	99
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.144	0.2	21
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.203	0.2	72
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.135	0.2	13
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.225	1.5	4209
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.265	2	5204
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.405	3	2642
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	0.634	4.5	2188
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	330	medium positional	0.99	0.5
1	2	C	330	medium positional	0.99	0.5
2	1	A	209	medium positional	0.08	0.5
2	2	C	209	medium positional	0.08	0.5
3	1	A	360	medium positional	0.2	0.5
4	1	B	330	medium positional	0.14	0.5
5	1	B	209	medium positional	0.17	0.5
5	2	D	209	medium positional	0.17	0.5
6	1	B	360	medium positional	0.28	0.5
6	2	D	360	medium positional	0.28	0.5
7	1	A	283	medium positional	0.15	0.5
7	2	B	283	medium positional	0.18	0.5
7	3	D	283	medium positional	0.13	0.5
8	1	A	209	medium positional	0.56	0.5
8	2	B	209	medium positional	0.34	0.5
8	3	D	209	medium positional	0.31	0.5
9	1	A	301	medium positional	0.38	0.5
9	2	B	301	medium positional	0.26	0.5
9	3	D	301	medium positional	0.35	0.5
1	1	A	452	loose positional	1.62	5
1	2	C	452	loose positional	1.62	5
2	1	A	263	loose positional	0.43	5
2	2	C	263	loose positional	0.43	5
3	1	A	435	loose positional	0.63	5
4	1	B	450	loose positional	0.6	5
5	1	B	263	loose positional	0.67	5
5	2	D	263	loose positional	0.67	5
6	1	B	435	loose positional	0.87	5
6	2	D	435	loose positional	0.87	5
7	1	A	388	loose positional	0.68	5
7	2	B	388	loose positional	0.79	5
7	3	D	388	loose positional	0.57	5
8	1	A	263	loose positional	1.01	5
8	2	B	263	loose positional	0.96	5
8	3	D	263	loose positional	0.7	5
9	1	A	365	loose positional	1	5
9	2	B	365	loose positional	0.8	5
9	3	D	365	loose positional	1.15	5
1	1	A	330	medium thermal	0.09	2
1	2	C	330	medium thermal	0.09	2
2	1	A	209	medium thermal	0.14	2
2	2	C	209	medium thermal	0.14	2
3	1	A	360	medium thermal	0.16	2
4	1	B	330	medium thermal	0.09	2
5	1	B	209	medium thermal	0.07	2
5	2	D	209	medium thermal	0.07	2
6	1	B	360	medium thermal	0.09	2
6	2	D	360	medium thermal	0.09	2
7	1	A	283	medium thermal	0.13	2
7	2	B	283	medium thermal	0.11	2
7	3	D	283	medium thermal	0.08	2
8	1	A	209	medium thermal	0.17	2
8	2	B	209	medium thermal	0.1	2
8	3	D	209	medium thermal	0.12	2
9	1	A	301	medium thermal	0.2	2
9	2	B	301	medium thermal	0.13	2
9	3	D	301	medium thermal	0.14	2
1	1	A	452	loose thermal	0.26	10
1	2	C	452	loose thermal	0.26	10
2	1	A	263	loose thermal	0.28	10
2	2	C	263	loose thermal	0.28	10
3	1	A	435	loose thermal	0.32	10
4	1	B	450	loose thermal	0.27	10
5	1	B	263	loose thermal	0.27	10
5	2	D	263	loose thermal	0.27	10
6	1	B	435	loose thermal	0.19	10
6	2	D	435	loose thermal	0.19	10
7	1	A	388	loose thermal	0.33	10
7	2	B	388	loose thermal	0.35	10
7	3	D	388	loose thermal	0.28	10
8	1	A	263	loose thermal	0.46	10
8	2	B	263	loose thermal	0.3	10
8	3	D	263	loose thermal	0.4	10
9	1	A	365	loose thermal	0.64	10
9	2	B	365	loose thermal	0.4	10
9	3	D	365	loose thermal	0.34	10

LS refinement shell

Resolution: 2.8→2.87 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.338	104
R_work	0.309	1846

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	18.7149	-2.9085	2.9796	4.5266	0.4388	5.5879	0.1248	0.013	-0.288	-0.163	-0.1106	0.0938	0.0723	-0.2344	-0.0143	-0.2539	-0.0765	0.0564	-0.2255	-0.1033	-0.1601	42.672	35.125	72.077
2	14.0836	7.0454	3.9072	9.9217	4.4455	7.8085	0.2718	-0.3118	-0.4733	0.2114	-0.085	-0.0922	0.3893	-0.1401	-0.1867	-0.2437	-0.0008	-0.0326	-0.1603	-0.0795	-0.2721	61.349	39.858	84.551
3	5.8636	1.642	4.2094	3.6197	2.7988	8.9504	0.4402	-0.719	-0.4803	0.8423	-0.109	-0.2899	0.9167	-0.2267	-0.3313	0.0429	0.01	-0.1376	-0.2259	-0.0269	-0.1542	74.114	47.573	101.984
4	8.729	-0.3873	1.3825	17.3825	1.7663	9.0854	0.0854	-0.5617	0.4592	0.8785	-0.2651	0.4296	-0.6176	-0.4471	0.1797	-0.166	-0.0505	-0.0311	-0.0627	0.0369	-0.1396	98.791	83.336	157.806
5	7.7411	2.495	5.1642	8.9081	5.2216	14.3489	0.2814	0.3837	-0.9029	-0.0739	0.1802	-0.3669	0.7805	0.5517	-0.4616	-0.1717	-0.0028	-0.0516	0.0542	-0.01	-0.169	98.705	65.909	142.421
6	3.5201	3.9367	7.5505	4.5016	7.8496	19.7625	0.079	0.3119	-0.3255	-0.6046	0.5878	0.07	0.3116	1.4725	-0.6668	0.0474	0.1356	-0.1534	0.0855	-0.1108	0.0348	89.798	59.902	120.872
7	11.6388	4.5417	-0.3842	8.0528	1.5909	4.3733	0.0737	0.723	0.3131	-0.4018	-0.0223	0.1569	0.1814	-0.3651	-0.0514	0.0111	0.0345	0.0666	-0.2204	0.0531	-0.1644	28.811	67.385	64.257
8	3.7643	2.2876	-1.9793	14.1739	3.3947	4.3212	0.3062	-0.1555	-0.0275	-0.0252	0.0064	-0.3403	0.306	0.4124	-0.3126	-0.0209	-0.0226	0.044	-0.2301	-0.0001	-0.2652	40.647	83.178	77.338
9	2.8584	0.5813	1.554	3.6238	2.0413	6.4345	0.1269	-0.3096	-0.2532	0.2743	-0.0505	-0.3131	0.4572	-0.1447	-0.0764	-0.1676	-0.0113	0.024	-0.2922	-0.0473	-0.2104	45.044	96.657	95.471
10	15.0009	-5.1909	-3.6579	8.9835	4.493	7.1593	0.0286	-0.0395	0.2427	0.1742	-0.2092	0.1329	-0.3642	-0.4138	0.1806	-0.0141	0.0898	-0.0113	-0.1328	-0.0103	-0.1781	42.495	139.465	151.859
11	6.4745	5.1718	3.5988	9.2521	10.7417	16.8825	0.3798	0.1595	-0.5021	0.1091	0.3918	-0.7811	0.3617	0.7535	-0.7716	-0.0512	0.0754	-0.0302	0.0147	-0.0769	-0.1695	52.873	126.642	135.357
12	0.5873	-1.3793	-2.5394	6.0446	5.2912	11.1402	0.0178	-0.3137	0.1386	-0.0626	0.2484	-0.184	-0.3828	0.1761	-0.2661	-0.1854	-0.0277	-0.023	-0.0318	-0.1366	-0.1535	49.143	115.82	114.281

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 68
2	X-RAY DIFFRACTION	2	A	69 - 103
3	X-RAY DIFFRACTION	3	A	104 - 165
4	X-RAY DIFFRACTION	4	B	3 - 68
5	X-RAY DIFFRACTION	5	B	69 - 103
6	X-RAY DIFFRACTION	6	B	104 - 164
7	X-RAY DIFFRACTION	7	C	3 - 68
8	X-RAY DIFFRACTION	8	C	69 - 103
9	X-RAY DIFFRACTION	9	C	104 - 164
10	X-RAY DIFFRACTION	10	D	3 - 68
11	X-RAY DIFFRACTION	11	D	69 - 103
12	X-RAY DIFFRACTION	12	D	104 - 164

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