PDB-2opt: Crystal Structure of Apo ActR from Streptomyces coelicolor.

ID or keywords:

Entry

Database: PDB / ID: 2opt

Title

Crystal Structure of Apo ActR from Streptomyces coelicolor.

Components

ActII protein

Keywords

TRANSCRIPTION / HELICAL PROTEIN / TETR FAMILY / APO-PROTEIN / TRANSCRIPTIONAL REPRESSOR

Function / homology

Function and homology information

response to antibiotic / negative regulation of DNA-templated transcription / DNA binding / metal ion binding
Similarity search - Function

Biological species

Streptomyces coelicolor (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.05 Å

Authors

Willems, A.R. / Junop, M.S.

Citation

Journal: J.Mol.Biol. / Year: 2008
Title: Crystal structures of the Streptomyces coelicolor TetR-like protein ActR alone and in complex with actinorhodin or the actinorhodin biosynthetic precursor (S)-DNPA.
Authors: Willems, A.R. / Tahlan, K. / Taguchi, T. / Zhang, K. / Lee, Z.Z. / Ichinose, K. / Junop, M.S. / Nodwell, J.R.

History

Deposition	Jan 30, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 5, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Derived calculations / Version format compliance
Revision 1.2	Dec 27, 2023	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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Download

PDBx/mmCIF format	2opt.cif.gz	182.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2opt.ent.gz	148.3 KB	Display	PDB format
PDBx/mmJSON format	2opt.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2opt_validation.pdf.gz	436.3 KB	Display	wwPDB validaton report
Full document	2opt_full_validation.pdf.gz	445.3 KB	Display
Data in XML	2opt_validation.xml.gz	20.9 KB	Display
Data in CIF	2opt_validation.cif.gz	30.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/op/2opt ftp://data.pdbj.org/pub/pdb/validation_reports/op/2opt	HTTPS FTP

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Related structure data

Related structure data	3b6aC 3b6cC C: citing same article (ref.)
Similar structure data	3b6c-d 3b6a-1 3b6a-2 3b6a-4 3b6a-3 2hxo-d 2xgc-2 2xgd-1 1gri-d 2xgc-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: ActII protein

B: ActII protein

50.4 kDa, 2 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)	55.648, 79.957, 104.027
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	ActII protein / Putative transcriptional regulatory protein Mass: 25200.555 Da / Num. of mol.: 2 / Fragment: N-terminal truncation (residues 30-259) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: M145 / Gene: actII / Plasmid: PROEX-HTA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q53901
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

ActII protein / Putative transcriptional regulatory protein

Mass: 25200.555 Da / Num. of mol.: 2 / Fragment: N-terminal truncation (residues 30-259)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Streptomyces coelicolor (bacteria) / Strain: M145 / Gene: actII / Plasmid: PROEX-HTA / Species (production host): Escherichia coli / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q53901

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.28 Å³/Da / Density % sol: 46.15 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 14% PEG4000, 91mM sodium acetate, 45mM Bis-Tris, 23mM KCl, 9.1mM EDTA, 4.6mM Tris, 0.45mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 8, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.1 Å / Relative weight: 1
Reflection	Resolution: 1.96→63.37 Å / Num. all: 34133 / Num. obs: 34133 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / B_iso Wilson estimate: 29 Å² / R_merge(I) obs: 0.055 / Net I/σ(I): 34.6
Reflection shell	Resolution: 1.96→2.03 Å / Redundancy: 7.2 % / R_merge(I) obs: 0.543 / Mean I/σ(I) obs: 3.85 / Num. unique all: 3351 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling
CNS		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.05→63.37 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.937 / SU B: 7.056 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.206 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24655	1507	5.1 %	RANDOM
R_work	0.19503	-	-	-
obs	0.19767	28206	99.62 %	-
all	-	28206	-	-

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: 44.921 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.11 Å²	0 Å²	0 Å²
2-	-	4.4 Å²	0 Å²
3-	-	-	-1.29 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→63.37 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3139	0	0	318	3457

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.021	3315
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.594	1.989	4513
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.998	5	443
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.831	23.289	152
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.665	15	573
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.953	15	34
X-RAY DIFFRACTION	r_chiral_restr	0.131	0.2	521
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	2534
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.232	0.2	1656
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.314	0.2	2296
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.161	0.2	267
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	0.256	0.2	90
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.229	0.2	20
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	0.999	1.5	2104
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.677	2	3365
X-RAY DIFFRACTION	r_scbond_it	2.499	3	1211
X-RAY DIFFRACTION	r_scangle_it	3.796	4.5	1133
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.05→2.103 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.336	114	-
R_work	0.229	2036	-
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	1.5423	0.4961	1.0232	1.2481	1.3644	8.5504	-0.0694	0.0782	0.0898	-0.1128	-0.1209	0.1596	-0.2944	-0.0105	0.1902	0.1607	0.0245	0.0087	0.0956	-0.0428	0.1766	-49.8743	15.574	-11.6711
2	3.1238	1.6435	3.1625	1.025	0.6116	10.1128	0.0172	-0.4293	0.1014	0.2248	0.0382	0.1203	0.1233	-0.7991	-0.0554	0.0984	0.0457	0.0464	0.1526	0.0096	0.1702	-53.5579	12.42	-1.6955
3	4.3419	-0.0841	0.9481	1.5465	-1.1696	4.7559	0.0204	-0.0527	-0.2397	-0.1317	0.0585	-0.0064	0.3157	-0.5738	-0.0789	0.1923	-0.0257	0.0176	0.078	-0.0452	0.1615	-52.1509	4.8653	-10.2294
4	8.5294	1.4092	-0.3267	1.1713	-0.1333	0.4166	-0.0441	0.2192	0.2147	-0.0407	0.0447	-0.1079	-0.0373	0.1177	-0.0005	0.1544	0.0205	0.0122	0.1175	-0.0074	0.1411	-27.4548	13.2282	-7.9719
5	7.8775	-0.2266	-0.9727	0.488	-0.0213	1.8234	0.113	-0.0321	0.0692	0.1746	-0.102	-0.1336	-0.0497	-0.0969	-0.011	0.1798	0.0053	-0.0105	0.0523	-0.0095	0.1661	-27.4454	13.7763	0.7436
6	8.4544	-2.6341	-2.1186	6.7088	7.329	10.7646	-0.2844	-0.4416	-0.5745	0.1301	0.0771	0.2898	1.2794	0.207	0.2074	0.2441	0.0511	0.0251	0.0616	0.0882	0.1678	-37.4814	2.5013	-1.3851
7	8.447	-0.7093	1.6273	0.7807	-0.6895	1.7724	0.0644	0.1759	0.0568	-0.0937	-0.0709	-0.0125	0.1128	0.0456	0.0065	0.1569	0.0311	0.0141	0.122	-0.0079	0.1458	-25.4266	6.9205	-11.3249
8	2.1608	-1.4762	-0.0482	1.4533	0.4722	3.5147	0.0908	0.0621	-0.2023	0.0624	-0.1197	0.0841	0.3268	0.0665	0.0289	0.1858	0.0372	-0.0233	0.0339	0.0091	0.1988	-20.2834	1.2907	-2.0761
9	16.0735	-6.3328	9.6842	28.0436	6.2894	9.8313	-0.69	-1.7125	-0.7717	1.3564	-0.5381	0.6262	0.2733	-0.9362	1.2281	0.2528	0.073	0.0637	0.2716	0.0324	0.0278	-32.7179	9.4613	10.3923
10	10.2304	-5.2035	1.9061	2.7269	-3.0474	54.1681	-0.8164	-0.0886	-0.5829	0.305	0.116	-0.1418	-1.4781	-3.9046	0.7004	0.71	-0.0253	0.1308	0.6961	-0.2706	0.5027	-35.7573	12.4212	20.6892
11	5.7139	-14.4377	3.8774	37.0655	-6.1016	25.9806	1.0759	-1.4832	0.7992	0.1973	-0.6229	0.6468	-1.0314	-0.4015	-0.453	0.1695	0.0396	0.21	0.0255	-0.1029	0.0648	-29.8671	8.1044	31.5427
12	4.9069	0.839	-2.4636	2.0928	-2.937	17.8973	0.5831	-0.8388	0.4027	-0.0436	0.1129	-0.1764	-0.4886	-0.2114	-0.696	0.1811	-0.0782	-0.0141	0.1206	-0.0131	0.0971	-21.6795	4.377	32.7648
13	3.1341	-6.1312	7.2929	15.9732	-22.9652	35.9854	-0.2851	-0.7801	-0.0346	0.6273	1.1673	0.1291	-1.244	-2.462	-0.8822	0.416	0.0475	-0.0121	0.2661	0.1025	0.1022	-26.1196	11.9477	20.0807
14	7.4719	-5.4656	-3.1022	4.4716	2.0938	7.4658	-0.181	-0.1159	-0.057	0.0547	0.1154	0.1042	-0.4735	0.1549	0.0656	0.2	-0.0203	-0.0382	0.0346	0.0333	0.1429	-20.452	10.956	10.1618
15	3.7319	-0.4065	3.8623	5.051	-5.2932	8.7392	0.1755	0.6369	-0.1428	-0.2115	-0.4757	-0.0213	0.0444	0.9376	0.3002	0.139	0.015	-0.0102	0.1869	0.0502	0.1484	-11.0222	3.2587	1.5838
16	418.4425	-102.8689	-290.994	112.94	163.8053	299.4919	-0.1955	-0.7881	-5.7569	1.6085	9.1748	-4.0463	-3.9242	4.9166	-8.9793	0.7293	0.025	-0.0008	0.6727	0.0409	0.7517	-2.7622	-3.1463	-4.0736
17	5.34	-0.4872	-3.3864	2.3535	2.8906	10.2721	-0.3149	-0.0044	-0.582	0.0898	-0.0249	0.1423	0.3788	-0.1417	0.3398	0.1551	0.0069	-0.0137	0.0804	-0.013	0.2077	-43.1324	-17.8106	27.5083
18	6.089	0.4855	-6.0341	2.0657	-0.1141	9.7527	-0.3092	1.1178	-0.4541	-0.1506	0.1525	0.3232	0.4555	-1.1707	0.1566	0.1361	-0.055	-0.0873	0.2379	-0.0879	0.1415	-50.1916	-16.1651	20.7144
19	5.2521	-0.2418	-2.484	0.2709	0.2595	1.5597	-0.0534	-0.0037	0.0689	-0.0983	0.0355	0.0097	-0.0897	-0.0958	0.0179	0.1764	0.0124	-0.0184	0.117	0.025	0.1269	-41.7174	-8.6071	25.3647
20	8.4916	1.869	1.0841	2.5955	2.7579	3.7337	0.1528	-0.2787	-0.5833	0.1047	0.0075	-0.1682	0.4929	0.7749	-0.1603	0.1449	0.0831	-0.0551	0.1837	0.0783	0.1535	-11.0011	-8.2361	21.016
21	9.1832	1.0653	-3.4296	0.248	-0.2381	3.5903	-0.1701	0.5844	-0.1985	0.0314	0.0331	-0.2178	0.2907	-0.3161	0.137	0.2411	0.0172	-0.0055	0.029	0.0208	0.1318	-27.875	-12.2235	14.202
22	2.2954	3.5066	3.6625	5.3569	5.595	5.8438	-0.4321	-0.09	1.2019	0.1909	-0.254	0.2011	-0.3947	-0.4732	0.6861	0.3957	0.0328	-0.0398	0.1617	0.1696	0.2464	-34.1994	-1.7329	19.0256
23	13.8861	4.6783	-0.6317	1.5803	-0.3195	2.7387	0.1072	-0.256	0.1553	0.3284	-0.1025	-0.1089	-0.0782	0.0852	-0.0047	0.2036	-0.0301	-0.0053	0.0926	0.0334	0.1252	-24.5458	-4.4962	28.0295
24	4.0337	1.2786	0.2117	2.2319	-0.1405	3.6905	0.3459	-0.1347	0.3122	-0.1084	-0.1535	0.006	-0.4383	0.6162	-0.1924	0.1922	-0.0796	0.0174	0.1089	0.0246	0.153	-15.3844	4.2221	21.2552
25	7.3624	4.5036	5.3252	5.8148	2.8177	3.9149	0.0933	0.0992	0.3236	-0.1244	-0.1914	0.129	-0.07	-0.5945	0.098	0.1864	0.0212	0.0237	0.078	0.0485	0.1752	-25.9668	-3.3798	11.3219
26	65.287	-8.8554	-6.287	24.6637	3.1143	0.8234	0.0682	2.6897	-0.52	-1.6408	-0.0412	1.0032	-0.0719	-2.2774	-0.0269	0.2843	-0.1278	-0.1265	0.3713	-0.0555	0.1096	-31.6003	-11.8217	2.8449
27	0.8887	4.9929	-4.4787	28.0506	-25.1615	22.57	-1.72	-3.4059	-1.5536	0.9541	1.9893	-0.1188	-0.1763	-1.7308	-0.2693	0.5863	0.0314	-0.0721	0.6384	-0.1537	0.7503	-33.9002	-12.5406	-7.0094
28	14.7395	-6.0324	-1.0857	19.9835	-6.8279	35.4784	0.7634	0.7719	-0.1775	-0.4488	-0.5485	-0.0018	1.6101	-0.7324	-0.2149	0.226	-0.169	-0.1309	-0.1466	-0.1401	0.1929	-31.8023	-7.1413	-14.4082
29	3.9608	-0.9747	1.0739	4.5187	-2.3176	9.3089	0.3183	0.4796	-0.4202	-0.1068	-0.0704	-0.1273	0.5	0.1431	-0.2479	0.1807	0.0693	0.0111	0.0787	-0.0783	0.1396	-23.9589	-1.0858	-17.2596
30	1.6371	0.641	0.1134	0.2509	0.0444	0.0079	-0.052	0.289	-0.9112	-1.1697	0.7468	0.4433	1.8399	-0.8011	-0.6948	0.4446	0.0054	-0.0176	0.1546	0.0081	0.2714	-24.5532	-9.6663	-4.3128
31	11.6158	11.3614	4.0262	13.405	1.6739	5.7343	0.0655	0.4394	-0.2994	-0.2404	0.0042	-0.4004	0.382	0.4641	-0.0697	0.1871	0.0844	0.0331	0.0692	0.0439	0.1684	-18.1571	-7.6833	4.627
32	1.0222	-1.491	-2.9758	7.5705	2.8749	9.0609	0.1535	-0.3538	-0.3539	0.3822	-0.115	-0.7957	0.0958	0.8388	-0.0385	0.1267	0.0159	-0.0351	0.2253	0.0711	0.1681	-10.5545	3.205	12.5681

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	27 - 43	2 - 18
2	X-RAY DIFFRACTION	2	A	A	44 - 62	19 - 37
3	X-RAY DIFFRACTION	3	A	A	63 - 80	38 - 55
4	X-RAY DIFFRACTION	4	A	A	81 - 99	56 - 74
5	X-RAY DIFFRACTION	5	A	A	100 - 121	75 - 96
6	X-RAY DIFFRACTION	6	A	A	122 - 131	97 - 106
7	X-RAY DIFFRACTION	7	A	A	132 - 146	107 - 121
8	X-RAY DIFFRACTION	8	A	A	147 - 169	122 - 144
9	X-RAY DIFFRACTION	9	A	A	170 - 174	145 - 149
10	X-RAY DIFFRACTION	10	A	A	175 - 193	150 - 168
11	X-RAY DIFFRACTION	11	A	A	194 - 200	169 - 175
12	X-RAY DIFFRACTION	12	A	A	201 - 216	176 - 191
13	X-RAY DIFFRACTION	13	A	A	217 - 222	192 - 197
14	X-RAY DIFFRACTION	14	A	A	223 - 233	198 - 208
15	X-RAY DIFFRACTION	15	A	A	234 - 242	209 - 217
16	X-RAY DIFFRACTION	16	A	A	243 - 245	218 - 220
17	X-RAY DIFFRACTION	17	B	B	29 - 46	4 - 21
18	X-RAY DIFFRACTION	18	B	B	47 - 64	22 - 39
19	X-RAY DIFFRACTION	19	B	B	65 - 90	40 - 65
20	X-RAY DIFFRACTION	20	B	B	91 - 104	66 - 79
21	X-RAY DIFFRACTION	21	B	B	105 - 124	80 - 99
22	X-RAY DIFFRACTION	22	B	B	125 - 131	100 - 106
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