PDB-3c2b: Crystal structure of TetR transcriptional regulator from Agrobact...

ID or keywords:

Entry

Database: PDB / ID: 3c2b

Title

Crystal structure of TetR transcriptional regulator from Agrobacterium tumefaciens

Components

Transcriptional regulator, TetR family

Transcriptional regulation

Keywords

TRANSCRIPTION REGULATOR /

structural genomics / APC5923 /

TetR /

transcription / PSI-2 /

Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

Biological species

Agrobacterium tumefaciens str. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.1 Å

Authors

Osipiuk, J. / Skarina, T. / Zheng, H. / 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 transcriptional regulator from Agrobacterium tumefaciens.
Authors: Osipiuk, J. / Skarina, T. / Zheng, H. / Savchenko, A. / Edwards, A.M. / Joachimiak, A.

History

Deposition	Jan 24, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 5, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3c2b.cif.gz	88.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3c2b.ent.gz	74.1 KB	Display	PDB format
PDBx/mmJSON format	3c2b.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/c2/3c2b ftp://data.pdbj.org/pub/pdb/validation_reports/c2/3c2b	HTTPS FTP

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Related structure data

Similar structure data	5ztc-d 6g87-1 6g8g-2 4fx5-d 5vlg-2 3dpj-3 3dpj-1 5fmp-d 5d1w-2 3aux-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: APC5923

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Transcriptional regulator, TetR family

B: Transcriptional regulator, TetR family

hetero molecules

48.7 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)	44.134, 72.791, 127.198
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Transcriptional regulator, TetR family / Transcriptional regulation Mass: 24310.102 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria) Species: Agrobacterium tumefaciens / Strain: C58 / Gene: Atu2020, AGR_C_3662 / Plasmid: modified pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A9CID8
#2: Chemical	ChemComp-FMT / FORMIC ACID / Formic acid Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH₂O₂
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.1 Å³/Da / Density % sol: 41.46 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 10.5 Details: 0.1 M CAPSO buffer, 20% PEG 2000 MME, 0.3 M NDSB-195, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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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: Feb 6, 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: 2.1→37.8 Å / Num. all: 23127 / Num. obs: 23127 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / B_iso Wilson estimate: 49.9 Å² / R_merge(I) obs: 0.081 / Χ²: 1.842 / Net I/σ(I): 10.5
Reflection shell	Resolution: 2.1→2.15 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.58 / Mean I/σ(I) obs: 1.86 / Num. unique all: 1024 / Χ²: 1.097 / % possible all: 60.4

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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
CNS		phasing
ARP/wARP		model building

Refinement

Method to determine structure:

SAD / Resolution: 2.1→37.8 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.946 / SU B: 11.444 / SU ML: 0.151 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.257 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2406	1190	5.2 %	RANDOM
R_work	0.1984	-	-	-
all	0.2006	23079	-	-
obs	0.2006	23079	93.48 %	-

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: 54.9 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.13 Å²	0 Å²	0 Å²
2-	-	-1.29 Å²	0 Å²
3-	-	-	-0.84 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→37.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3058	0	6	92	3156

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.021	3143
X-RAY DIFFRACTION	r_angle_refined_deg	1.486	1.977	4225
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.602	5	401
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.835	22.288	153
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.776	15	566
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.781	15	41
X-RAY DIFFRACTION	r_chiral_restr	0.107	0.2	471
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	2373
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	1518
X-RAY DIFFRACTION	r_nbtor_refined	0.302	0.2	2180
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.172	0.2	126
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.214	0.2	56
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.188	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	0.915	1.5	2030
X-RAY DIFFRACTION	r_mcangle_it	1.44	2	3085
X-RAY DIFFRACTION	r_scbond_it	2.189	3	1251
X-RAY DIFFRACTION	r_scangle_it	3.36	4.5	1134

LS refinement shell

Resolution: 2.1→2.154 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.322	65	-
R_work	0.247	988	-
all	-	1053	-
obs	-	1053	59.66 %

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	4.1952	-4.4596	0.3879	11.2789	-8.8345	10.8846	-0.0857	-0.4859	-0.3201	0.849	-0.1204	-0.1563	-0.0829	0.3655	0.206	0.5178	-0.1172	-0.112	-0.0492	0.0845	-0.2647	38.5214	27.8648	128.0284
2	15.3224	4.2402	7.4569	7.7705	2.1882	21.4756	0.096	1.1019	-0.9758	0.5397	0.4633	0.1226	1.1725	0.5963	-0.5593	0.2028	0.2658	0.2276	-0.3965	0.1847	0.0051	39.7618	25.0774	114.1853
3	1.789	1.5881	4.974	4.1477	4.864	13.903	0.1418	0.2991	-0.4606	0.3732	0.3507	0.0017	0.7231	0.7601	-0.4924	-0.0264	0.032	0.0296	-0.1134	-0.014	-0.0382	30.5964	31.4829	101.4299
4	25.8045	4.6183	18.4403	9.6725	8.2113	15.9041	-0.2605	-0.0546	-0.8036	-0.5332	0.2841	-0.1074	0.6054	1.5974	-0.0236	0.0929	0.2012	0.0645	0.4242	0.0755	0.0647	44.5855	31.2599	107.7171
5	6.7852	-1.3054	12.1709	3.0107	3.949	40.0914	-0.1794	0.1234	-0.6281	0.2094	0.1035	0.0091	1.1761	0.583	0.0759	-0.0016	0.0915	0.0417	-0.2463	-0.0463	0.0596	35.5467	26.4757	93.2136
6	4.3996	6.1607	5.8952	10.5476	9.1944	11.7527	-0.2357	0.2292	-0.0519	-0.5401	0.5655	-0.4601	-0.3278	0.7271	-0.3298	-0.0715	0.0611	0.0611	-0.1429	-0.0301	-0.1536	36.6389	32.4365	84.8862
7	0.815	1.0206	2.3798	5.0474	2.4872	7.0138	-0.0735	-0.0155	-0.0253	0.0782	0.0573	0.4052	0.1416	-0.0667	0.0163	-0.079	-0.0017	0.0469	-0.1106	-0.0071	-0.0404	31.2675	41.678	102.2524
8	14.5072	-1.6817	14.0897	17.8238	9.5749	20.8103	-0.0011	-0.4519	-0.0202	0.116	-0.4703	2.8619	-2.0237	-1.0799	0.4715	-0.1283	-0.0652	0.1025	-0.032	-0.0558	0.1202	21.6577	41.6859	108.0314
9	1.5061	-1.2456	-3.4865	2.0489	1.5624	9.7852	0.1154	0.2737	-0.0482	-0.6292	-0.165	0.8059	0.168	-0.569	0.0496	0.0517	0.0033	-0.1225	-0.1255	-0.013	0.0178	24.4803	35.5255	85.7138
10	1.144	2.1628	-1.4401	15.5513	-0.9382	7.4066	0.3281	-0.194	0.1023	-0.0062	0.0245	0.2231	-0.3341	0.1404	-0.3526	-0.021	-0.1801	-0.1249	-0.041	-0.0388	-0.1814	45.5876	62.267	121.0255
11	14.4929	13.9492	8.1713	14.2595	6.8727	13.9912	0.1932	-2.4911	1.0878	0.6724	-1.5125	1.4209	-0.2186	-1.8639	1.3192	0.0225	-0.1234	-0.0034	0.1078	-0.2536	-0.0737	38.7062	66.4655	127.0072
12	17.8192	0.0535	-3.2616	11.7109	-7.4824	21.5981	-0.8715	1.4175	0.2428	-0.1376	0.2201	-0.1009	-1.0137	-0.8201	0.6514	-0.0949	-0.1655	-0.1226	-0.1364	-0.005	-0.2349	38.3072	62.32	112.4891
13	0.4952	-0.8685	1.0195	2.8899	-2.2127	4.1086	0.122	0.0535	0.1973	0.0592	-0.0304	-0.1048	-0.4912	0.5293	-0.0916	-0.0518	-0.125	0.0248	-0.0878	-0.008	-0.1438	38.8424	55.6177	97.6562
14	6.7614	-3.4363	-6.1206	8.3455	-3.0366	16.8548	0.0864	-0.1353	0.1023	0.9321	-0.3921	0.6845	-0.7264	0.0139	0.3057	0.0189	-0.0244	0.0186	-0.2917	-0.0714	-0.269	30.6294	48.2556	117.8986
15	3.7398	-4.2973	3.3294	5.844	-1.9219	6.9645	-0.0548	-0.2839	0.3235	-0.1416	-0.2466	0.0663	-0.1364	-0.144	0.3014	0.0744	-0.0692	0.0022	-0.1332	-0.037	-0.0819	28.6674	59.8205	97.5452
16	0.2092	-0.2522	0.2605	0.3046	-0.2764	2.4792	-0.0408	0.1123	-0.2598	-0.1051	0.0032	0.1941	-0.296	0.1744	0.0376	-0.03	-0.0072	-0.0285	-0.1124	0.006	-0.0698	31.7256	48.3353	95.6795
17	3.9676	6.8777	-2.0876	35.1059	-29.4893	29.9671	-0.7323	-0.0511	-0.5228	-1.5342	-1.1918	-2.2333	1.9757	1.2563	1.9241	-0.0405	0.2722	0.292	0.2352	0.2091	-0.0625	47.9959	45.6961	97.9347
18	0.7307	-0.516	1.473	2.4764	-0.1641	3.333	-0.019	0.221	-0.1718	-0.6876	-0.1218	-0.0196	-0.1491	0.2223	0.1408	0.0802	0.0053	0.0306	-0.0969	-0.0392	-0.1458	33.3655	50.9947	82.6511

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	12 - 52	14 - 54
2	X-RAY DIFFRACTION	2	A	A	53 - 78	55 - 80
3	X-RAY DIFFRACTION	3	A	A	79 - 119	81 - 121
4	X-RAY DIFFRACTION	4	A	A	124 - 135	126 - 137
5	X-RAY DIFFRACTION	5	A	A	136 - 148	138 - 150
6	X-RAY DIFFRACTION	6	A	A	149 - 164	151 - 166
7	X-RAY DIFFRACTION	7	A	A	165 - 180	167 - 182
8	X-RAY DIFFRACTION	8	A	A	181 - 187	183 - 189
9	X-RAY DIFFRACTION	9	A	A	188 - 214	190 - 216
10	X-RAY DIFFRACTION	10	B	B	11 - 43	13 - 45
11	X-RAY DIFFRACTION	11	B	B	44 - 59	46 - 61
12	X-RAY DIFFRACTION	12	B	B	60 - 72	62 - 74
13	X-RAY DIFFRACTION	13	B	B	80 - 116	82 - 118
14	X-RAY DIFFRACTION	14	B	B	117 - 130	119 - 132
15	X-RAY DIFFRACTION	15	B	B	131 - 151	133 - 153
16	X-RAY DIFFRACTION	16	B	B	152 - 181	154 - 183
17	X-RAY DIFFRACTION	17	B	B	182 - 188	184 - 190
18	X-RAY DIFFRACTION	18	B	B	189 - 212	191 - 214

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