PDB-3bni: Crystal structure of TetR-family transcriptional regulator from S...

ID or keywords:

Entry

Database: PDB / ID: 3bni

Title

Crystal structure of TetR-family transcriptional regulator from Streptomyces coelicolor

Components

Putative TetR-family transcriptional regulator

Keywords

TRANSCRIPTION REGULATOR /

structural genomics / APC7281 / TetR transcriptional regulator / PSI-2 /

Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / DNA-binding /

Transcription regulation

Function / homology

Function and homology information

transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function

Biological species

Streptomyces coelicolor A3

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.3 Å

Authors

Osipiuk, J. / Xu, X. / Gu, J. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: X-ray crystal structure of TetR-family transcriptional regulator from Streptomyces coelicolor.
Authors: Osipiuk, J. / Xu, X. / Gu, J. / Savchenko, A. / Edwards, A.M. / Joachimiak, A.

History

Deposition	Dec 14, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 25, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3	Feb 21, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3bni.cif.gz	85 KB	Display	PDBx/mmCIF format
PDB format	pdb3bni.ent.gz	65 KB	Display	PDB format
PDBx/mmJSON format	3bni.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

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

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Related structure data

Similar structure data	3vs7-2 2ffh-2 3lmm-3 4lue-2 3vs2-2 2ffh-1 3vrz-1 4ckw-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: APC7281

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative TetR-family transcriptional regulator

B: Putative TetR-family transcriptional regulator

hetero molecules

51.9 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)	46.091, 66.354, 125.083
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Putative TetR-family transcriptional regulator Mass: 25776.082 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria) Species: Streptomyces coelicolorStreptomyces albidoflavus / Strain: A3(2) / M145 / Gene: SCO1712, SCI11.01c, SCI30A.33c / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8CK21
#2: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 80 / 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: 1.86 Å³/Da / Density % sol: 33.7 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M Bis-Tris buffer, 0.2 M Ammonium sulfate, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 9, 2006
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.3→38 Å / Num. all: 17771 / Num. obs: 17771 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / B_iso Wilson estimate: 50.5 Å² / R_merge(I) obs: 0.082 / Χ²: 1.084 / Net I/σ(I): 9
Reflection shell	Resolution: 2.3→2.37 Å / Redundancy: 6.4 % / R_merge(I) obs: 0.807 / Mean I/σ(I) obs: 2.38 / Num. unique all: 1402 / Χ²: 1.118 / % possible all: 98

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC		refinement
PDB_EXTRACT	3.004	data extraction
SBC-Collect		data collection
HKL-2000		data reduction
SHELXD		phasing
MLPHARE		phasing
DM		phasing
SOLVE		phasing
RESOLVE		phasing
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.3→38 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.93 / SU B: 14.567 / SU ML: 0.176 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.332 / ESU R Free: 0.239 / 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	904	5.1 %	RANDOM
R_work	0.197	-	-	-
all	0.2	17716	-	-
obs	0.2	17716	99.7 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 34.088 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.62 Å²	0 Å²	0 Å²
2-	-	0.58 Å²	0 Å²
3-	-	-	0.04 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→38 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2726	0	26	80	2832

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	2783
X-RAY DIFFRACTION	r_angle_refined_deg	1.6	1.992	3745
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.393	5	341
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.748	21.818	143
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.755	15	478
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.361	15	45
X-RAY DIFFRACTION	r_chiral_restr	0.126	0.2	423
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	2111
X-RAY DIFFRACTION	r_nbd_refined	0.216	0.2	1312
X-RAY DIFFRACTION	r_nbtor_refined	0.304	0.2	1914
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.164	0.2	126
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.208	0.2	65
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.217	0.2	15
X-RAY DIFFRACTION	r_mcbond_it	0.852	1.5	1758
X-RAY DIFFRACTION	r_mcangle_it	1.398	2	2705
X-RAY DIFFRACTION	r_scbond_it	2.372	3	1144
X-RAY DIFFRACTION	r_scangle_it	3.846	4.5	1040

LS refinement shell

Resolution: 2.3→2.36 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.297	52	-
R_work	0.234	1171	-
all	-	1223	-
obs	-	1223	96.91 %

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	11.8864	8.2184	-7.3276	15.8584	-7.538	5.1176	-0.9196	0.4159	-0.5475	-0.0644	0.3252	-0.2858	0.4133	0.3996	0.5944	0.0974	0.0226	-0.0114	0.0105	-0.0976	0.0813	-8.2592	-12.8919	9.5499
2	8.8198	3.4597	3.3885	7.7016	0.9914	1.5336	-0.111	0.8211	0.1279	-0.6968	0.1475	0.0721	-0.3325	0.5732	-0.0366	0.1033	0.0017	-0.0219	0.1872	0.0611	-0.0072	-5.3972	-2.0689	0.6639
3	4.7446	2.7676	-1.0036	3.136	-0.8882	7.0741	0.3233	-0.581	0.3875	-0.2357	0.0459	0.556	0.0007	-0.288	-0.3692	-0.0492	-0.061	-0.0585	0.1591	0.078	0.1059	-14.5628	-7.2148	5.5551
4	24.2866	-6.0209	22.8658	3.328	-6.3694	21.7957	0.2213	0.354	-0.1567	0.2579	-0.1671	0.2522	0.0713	0.2284	-0.0542	0.0455	-0.014	-0.0057	0.0113	-0.0546	0.0987	0.6498	-3.2308	18.5583
5	6.2239	-0.9665	6.9847	0.8061	0.0165	9.6871	0.0381	0.0518	-0.1305	-0.0988	0.1677	-0.1281	0.01	-0.0128	-0.2057	0.1037	-0.0362	-0.0324	-0.0221	0.0147	0.129	15.4205	-0.0851	26.3049
6	0.668	0.8854	1.8095	4.0435	4.0118	5.8086	0.1289	-0.1517	-0.2135	-0.1992	-0.2448	0.0795	-0.3198	-0.211	0.1159	0.0768	-0.0262	-0.0065	0.114	-0.0943	0.083	9.1987	-0.4965	11.1292
7	10.6599	12.0036	1.4351	26.6099	-9.3945	9.4523	-1.7517	0.8816	-0.1345	-0.0207	0.2641	0.0301	-1.6101	0.6486	1.4876	0.1116	-0.0344	-0.0057	-0.008	-0.0206	0.1897	1.5495	3.6559	12.2176
8	20.4292	-14.8591	19.3174	13.5329	-14.0271	30.498	0.2697	-0.9716	-0.0959	-0.3927	0.1486	0.373	0.2447	-1.2009	-0.4183	-0.0068	-0.0848	0.0267	0.0265	-0.039	0.0941	2.4621	3.272	28.7779
9	7.3434	-6.4364	-2.7822	7.1087	2.5924	8.4199	-0.0932	-0.5808	-0.3028	0.6095	0.1324	0.776	-0.2728	0.154	-0.0392	0.0805	-0.0382	0.0303	0.0386	0.0311	0.0472	6.7576	8.1209	36.9951
10	0.8438	-0.9769	-2.9978	2.8005	2.9814	10.7937	-0.0071	0.245	0.0081	-0.1429	-0.1861	0.1425	-0.2465	-0.6382	0.1932	0.0753	0.0203	-0.0138	0.0839	-0.0298	0.1072	10.0941	11.4084	15.8233
11	0.6868	0.9089	-0.278	1.2046	-0.523	14.6639	0.0313	-0.1154	-0.6063	-0.0608	0.1311	-0.8665	0.3097	0.4689	-0.1623	0.0945	0.0421	0.0631	0.0206	-0.0563	0.1988	20.0033	10.0349	14.7276
12	9.0773	0.692	-0.0549	1.3659	-1.0657	20.1931	-0.1692	-0.2976	-0.4833	0.2667	0.2683	-0.1952	0.0857	-0.0065	-0.0991	0.1129	0.0414	0.0042	-0.0277	0.0209	0.124	17.5649	12.8923	30.1033
13	1.2349	-1.5875	2.8726	2.2343	-4.8257	13.3104	-0.2167	-0.2381	0.437	0.4356	-0.0713	-0.1397	-0.8086	-0.5071	0.288	0.1476	0.0913	-0.0285	0.0701	-0.0209	0.0845	-3.7423	42.128	4.6969
14	6.5419	-1.2864	2.1848	11.7795	-4.6838	11.0745	0.7595	-0.8217	-0.9847	0.0992	-0.0618	0.5762	0.0448	-1.1287	-0.6978	0.079	-0.203	0.0138	0.1524	0.0938	-0.0463	-9.1349	30.5758	7.2868
15	2.1946	-0.6079	3.1175	7.6153	-3.9877	20.3067	0.0938	0.1289	0.21	0.0175	0.1129	0.3181	-0.8094	-1.9541	-0.2067	0.0759	0.124	0.003	0.1746	0.0037	-0.0007	-10.5705	40.9546	0.0267
16	6.4771	-3.4205	-0.9353	1.8328	-0.1038	13.6709	0.0481	0.6014	0.0959	0.191	-0.0883	-0.0172	0.192	-0.1588	0.0402	0.0659	0.0157	-0.0303	0.0718	0.0117	-0.0023	-2.0641	34.357	-3.8537
17	12.2503	2.5938	11.7356	1.5384	2.2418	11.3023	-0.4396	0.2859	0.3217	0.0747	-0.0703	-0.0768	-0.506	-0.0733	0.5099	0.1185	0.0014	-0.0347	0.0219	0.0506	0.0373	9.8094	37.765	12.6252
18	13.6259	-0.3569	3.8617	0.4941	0.5601	1.9963	0.3515	0.195	0.3321	0.0765	-0.3183	-0.1498	-0.1118	-0.079	-0.0332	0.1269	-0.0027	0.0242	0.0249	0.0206	0.065	12.1992	33.6816	23.3247
19	25.9205	-12.6623	2.0564	6.1863	-1.0019	0.1751	-0.71	0.509	-1.2734	0.185	-0.0891	0.3829	0.4073	-0.1517	0.7991	0.1855	-0.0498	-0.0083	0.0714	0.0756	0.1061	6.4873	28.696	11.0294
20	35.2641	7.2283	14.2801	4.7986	-3.0982	16.7272	0.1179	1.268	0.1344	0.1019	0.6984	0.1707	-0.5113	0.9081	-0.8164	0.1331	-0.0669	0.0347	0.0625	0.0364	0.0071	20.7601	31.6323	12.4764
21	3.1118	3.4704	0.3345	3.9442	0.7761	2.2361	-0.362	0.2718	0.1474	-0.5331	0.2817	0.2154	-0.0121	0.2344	0.0803	0.059	-0.0008	0.0071	0.0623	0.0073	0.1064	25.3783	25.0708	14.5642
22	4.2883	-0.8394	-1.7595	0.1644	0.3609	3.1851	-0.0005	0.1664	0.0796	-0.2122	-0.0138	0.1685	0.01	-0.1419	0.0143	0.1423	-0.0058	-0.0178	0.0026	-0.0175	0.1165	6.9496	21.8209	20.115
23	2.748	-2.0826	-2.9506	19.7604	2.1173	3.1689	-0.2277	0.1388	0.102	1.0199	-0.2333	0.5335	-0.3077	-1.1257	0.4609	0.0846	0.0694	0.1365	0.068	-0.0183	0.1273	-0.9173	24.5502	28.8309
24	18.1273	0.5683	-3.4653	0.5423	-0.7601	1.4718	0.084	-0.0229	-0.0262	0.328	-0.0272	-0.2088	-0.2878	-0.0371	-0.0567	0.1716	-0.0247	-0.0243	-0.0067	0.006	0.0713	16.337	21.6539	27.5202

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	18 - 29	40 - 51
2	X-RAY DIFFRACTION	2	A	A	30 - 50	52 - 72
3	X-RAY DIFFRACTION	3	A	A	51 - 65	73 - 87
4	X-RAY DIFFRACTION	4	A	A	66 - 88	88 - 110
5	X-RAY DIFFRACTION	5	A	A	89 - 107	111 - 129
6	X-RAY DIFFRACTION	6	A	A	108 - 116	130 - 138
7	X-RAY DIFFRACTION	7	A	A	117 - 123	139 - 145
8	X-RAY DIFFRACTION	8	A	A	138 - 148	160 - 170
9	X-RAY DIFFRACTION	9	A	A	149 - 162	171 - 184
10	X-RAY DIFFRACTION	10	A	A	163 - 183	185 - 205
11	X-RAY DIFFRACTION	11	A	A	184 - 193	206 - 215
12	X-RAY DIFFRACTION	12	A	A	194 - 205	216 - 227
13	X-RAY DIFFRACTION	13	B	B	21 - 33	43 - 55
14	X-RAY DIFFRACTION	14	B	B	34 - 44	56 - 66
15	X-RAY DIFFRACTION	15	B	B	45 - 58	67 - 80
16	X-RAY DIFFRACTION	16	B	B	59 - 67	81 - 89
17	X-RAY DIFFRACTION	17	B	B	68 - 89	90 - 111
18	X-RAY DIFFRACTION	18	B	B	90 - 116	112 - 138
19	X-RAY DIFFRACTION	19	B	B	117 - 140	139 - 162
20	X-RAY DIFFRACTION	20	B	B	141 - 149	163 - 171
21	X-RAY DIFFRACTION	21	B	B	150 - 164	172 - 186
22	X-RAY DIFFRACTION	22	B	B	165 - 178	187 - 200
23	X-RAY DIFFRACTION	23	B	B	179 - 187	201 - 209
24	X-RAY DIFFRACTION	24	B	B	188 - 204	210 - 226

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