PDB-3bru: Crystal structure of regulatory protein TetR from Rhodobacter sph...

ID or keywords:

Entry

Database: PDB / ID: 3bru

Title

Crystal structure of regulatory protein TetR from Rhodobacter sphaeroides

Components

Regulatory protein, TetR family

Keywords

TRANSCRIPTION / structural genomics / APC88928 / TetR / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / DNA-binding / Transcription regulation

Function / homology

Function and homology information

Biological species

Rhodobacter sphaeroides 2.4.1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.3 Å

Authors

Osipiuk, J. / Maltseva, N. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of regulatory protein TetR from Rhodobacter sphaeroides.
Authors: Osipiuk, J. / Maltseva, N. / Freeman, L. / Joachimiak, A.

History

Deposition	Dec 21, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 8, 2008	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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3bru.cif.gz	89.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3bru.ent.gz	75.2 KB	Display	PDB format
PDBx/mmJSON format	3bru.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3bru_validation.pdf.gz	432.2 KB	Display	wwPDB validaton report
Full document	3bru_full_validation.pdf.gz	434.7 KB	Display
Data in XML	3bru_validation.xml.gz	16.5 KB	Display
Data in CIF	3bru_validation.cif.gz	23.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/br/3bru ftp://data.pdbj.org/pub/pdb/validation_reports/br/3bru	HTTPS FTP

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Related structure data

Similar structure data	6azh-d 2hq5-1 3g7r-d 4uds-1 6of0-2 1rpw-1 1vi0-d 1rkw-1 4nel-1 2g3b-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: APC88928

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Regulatory protein, TetR family

B: Regulatory protein, TetR family

50 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)	63.416, 82.564, 91.316
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Regulatory protein, TetR family Mass: 25000.785 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides 2.4.1 (bacteria) Species: Rhodobacter sphaeroides / Strain: 2.4.1 / NCIB 8253 / DSM 158 / Gene: RSP_1435, RHOS4_00080 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q3J6K8
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Regulatory protein, TetR family

Mass: 25000.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Rhodobacter sphaeroides 2.4.1 (bacteria)
Species: Rhodobacter sphaeroides / Strain: 2.4.1 / NCIB 8253 / DSM 158 / Gene: RSP_1435, RHOS4_00080 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q3J6K8

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.39 Å³/Da / Density % sol: 48.55 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG 3000, 0.1 M HEPES buffer, 0.2 M Sodium chloride, pH 7.5, VAPOR DIFFUSION, SITTING 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: Nov 5, 2007
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→40 Å / Num. all: 21647 / Num. obs: 21647 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.5 % / B_iso Wilson estimate: 48.3 Å² / R_merge(I) obs: 0.183 / Χ²: 1.645 / Net I/σ(I): 6.3
Reflection shell	Resolution: 2.3→2.38 Å / Redundancy: 6.5 % / R_merge(I) obs: 0.67 / Mean I/σ(I) obs: 1.95 / Num. unique all: 2068 / Χ²: 1.612 / % possible all: 96.7

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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-3000		data reduction
SHELXD		phasing
MLPHARE		phasing
DM		phasing
SOLVE		phasing
RESOLVE		phasing
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.3→40 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.948 / SU B: 11.857 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.257 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2007	1100	5.1 %	RANDOM
R_work	0.1685	-	-	-
all	0.1702	21442	-	-
obs	0.1702	21442	98.38 %	-

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: 25.982 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.9 Å²	0 Å²	0 Å²
2-	-	0.02 Å²	0 Å²
3-	-	-	-1.92 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3011	0	0	155	3166

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.021	3101
X-RAY DIFFRACTION	r_angle_refined_deg	1.548	1.949	4186
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.979	5	382
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.772	21.698	159
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.48	15	505
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.62	15	38
X-RAY DIFFRACTION	r_chiral_restr	0.113	0.2	438
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	2424
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	1301
X-RAY DIFFRACTION	r_nbtor_refined	0.304	0.2	2150
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.168	0.2	123
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.209	0.2	30
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.298	0.2	14
X-RAY DIFFRACTION	r_mcbond_it	0.856	1.5	1942
X-RAY DIFFRACTION	r_mcangle_it	1.29	2	2967
X-RAY DIFFRACTION	r_scbond_it	2.433	3	1321
X-RAY DIFFRACTION	r_scangle_it	4.069	4.5	1217

LS refinement shell

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

	R_factor	Num. reflection	% reflection
R_free	0.316	71	-
R_work	0.216	1359	-
all	-	1430	-
obs	-	1430	90.22 %

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	13.6894	-0.0586	0.907	30.9918	-4.8893	19.4201	-0.0762	-1.7491	0.4084	2.1578	0.3547	-0.0942	-0.8188	-0.1136	-0.2785	0.2615	0.0368	0.0061	0.376	0.0289	0.1457	8.9415	65.8244	18.7128
2	0.4169	1.0317	1.9374	10.9183	8.7017	10.8284	-0.0122	0.0517	0.001	-0.0925	-0.1264	0.1062	0.2554	-0.1898	0.1386	0.1644	-0.0038	0.0063	0.2897	-0.0077	0.0903	6.8233	55.4187	8.5746
3	1.2269	-0.5471	-0.6194	3.687	3.0954	7.3701	-0.1384	0.0047	0.1583	0.0145	0.1416	0.2423	0.1177	0.0029	-0.0032	0.1212	0.0307	-0.0204	0.2403	-0.0131	0.1291	1.7703	64.3382	8.9838
4	5.3092	-7.5789	-0.414	12.9747	6.8997	18.4952	0.5351	0.0515	-0.1339	-0.3672	0.3633	-0.1418	-0.3877	0.4035	-0.8984	0.1664	-0.0182	-0.0095	0.1613	-0.0609	0.1748	10.3944	71.9207	8.348
5	2.5313	-2.3769	-1.4169	2.8562	2.091	1.7197	-0.0827	-0.1508	-0.0512	-0.1924	0.0218	-0.2873	-0.0599	-0.0504	0.0608	0.1879	-0.0141	0.0208	0.2433	-0.0094	0.08	12.7956	64.2844	3.5939
6	5.0699	-4.3623	1.6853	6.3045	-1.9958	1.1296	0.0012	-0.0964	-0.0189	0.1584	0.0902	0.1245	-0.1511	0.0684	-0.0913	0.1922	-0.0157	0.0229	0.2491	-0.0365	0.0724	23.6256	49.7974	12.6502
7	16.5315	-4.2413	7.1954	1.0881	-1.846	3.1319	0.2052	-0.2009	-0.0062	-0.0261	-0.1064	0.0972	0.1263	0.0926	-0.0988	0.263	-0.0049	-0.0281	0.1832	0.0395	0.0616	25.5706	36.6779	12.4589
8	1.4485	1.073	-1.8247	1.3007	-1.8341	3.3368	-0.059	-0.0644	0.1136	0.0453	0.0733	-0.1079	0.0817	0.0202	-0.0144	0.1876	0.0307	0.0193	0.2078	0.0001	0.0892	10.0896	45.864	7.5282
9	15.2558	6.169	8.5638	7.757	5.3724	6.0148	-0.2986	0.1099	0.001	-0.4574	-0.0348	0.2099	-0.6002	0.353	0.3334	0.1977	0.0089	-0.0098	0.1876	0.0037	0.0516	13.023	59.9557	-6.767
10	5.6696	-3.9803	1.8411	2.8774	-1.6524	2.1582	0.1079	-0.0358	-0.0298	0.1357	-0.1213	-0.1808	-0.2115	0.1515	0.0134	0.1737	0.0216	0.0126	0.1567	-0.0141	0.0795	20.523	56.5016	-2.7033
11	8.7118	-6.4142	-1.8637	8.4398	0.774	1.4523	-0.2316	-0.0665	0.3569	-0.0024	0.1103	-0.2869	0.0849	0.1562	0.1213	0.1743	-0.0327	-0.0081	0.1889	0.0017	0.0557	31.1054	44.9302	4.1044
12	9.6231	-3.9575	-5.3488	4.5237	-5.6914	24.4738	-0.6224	0.2968	-0.742	-0.1601	-0.9248	0.0029	3.1956	1.6401	1.5472	0.7319	0.0484	0.193	0.528	0.0165	0.4411	36.7911	33.0984	1.2515
13	7.7013	-6.225	-1.415	9.0569	-0.3523	1.3819	0.1531	0.7991	0.1676	-0.2346	0.0005	-0.3792	0.0392	-0.2271	-0.1536	0.1871	-0.0151	-0.015	0.1623	-0.0187	0.0657	27.4721	41.4921	-1.4014
14	1.8519	-0.6588	-1.1644	0.2354	0.37	2.5956	0.0029	0.0809	-0.1075	0.0268	0.0254	0.0222	0.1314	-0.1177	-0.0283	0.2182	-0.0118	-0.0152	0.1689	-0.0017	0.1011	11.4135	37.5587	2.1965
15	15.7243	-0.8194	-7.2698	17.1054	5.6328	8.6984	0.4266	-1.1549	-0.1123	0.3014	0.053	-0.9893	0.2037	0.2277	-0.4796	0.2995	0.0707	-0.0019	0.1838	0.0577	0.0774	24.9229	29.4907	0.8752
16	24.4777	0.5078	3.2523	17.9362	-0.1341	0.7848	0.2169	1.583	-0.2387	-0.5939	-0.3013	0.715	0.3087	0.598	0.0843	0.1886	0.0958	0.0289	0.2535	-0.0652	0.0628	-4.6781	50.4426	-25.0337
17	26.4895	7.75	12.1559	16.0891	1.65	13.387	0.096	-0.2257	0.7671	-0.1396	-0.4628	0.4004	-0.2239	0.1347	0.3669	0.1131	-0.0164	0.003	0.2189	-0.0134	0.0622	4.5752	52.6678	-15.5883
18	5.8725	-5.2674	7.1078	6.129	-4.1963	11.9842	-0.3257	-0.1504	0.4424	0.5147	0.1305	-0.1444	-0.8301	0.0491	0.1952	0.1083	0.0153	0.0198	0.2953	-0.0203	0.0922	-2.3805	56.6856	-10.6966
19	4.7453	-1.2523	-0.5318	7.3989	1.4269	5.545	-0.0258	-0.0645	0.1026	-0.1958	-0.0635	-0.4744	-0.087	-0.061	0.0892	0.1752	0.0267	-0.0093	0.1596	0.0062	0.0778	-6.2408	59.2705	-21.4803
20	11.0544	2.6198	2.4167	2.8542	0.1461	9.0646	0.0812	0.2745	-0.546	0.2313	0.2439	0.1862	0.5478	-0.2269	-0.3251	0.1429	0.0328	0.009	0.1217	-0.0441	0.1099	-12.601	51.4067	-16.0503
21	5.3012	-6.2815	-2.7438	7.7148	2.8957	1.8853	-0.0371	-0.1103	-0.2688	-0.3245	-0.0787	0.3315	0.0217	-0.1459	0.1157	0.1706	0.0164	-0.0209	0.2187	-0.0281	0.0808	-3.4644	44.04	-14.5864
22	4.7255	-2.563	-1.5186	1.394	0.5649	17.6564	0.1685	0.2709	-0.1966	-0.2969	0.3861	-0.1998	-1.1353	0.1232	-0.5546	0.2458	0.0056	0.0234	0.1611	-0.017	0.1182	5.9657	36.0961	-21.5842
23	9.7332	-4.9604	-1.7541	4.7557	2.4579	1.4141	-0.1684	-0.1293	-0.1117	-0.1221	0.1765	-0.0951	-0.026	-0.2531	-0.0081	0.2035	-0.0153	0.0268	0.1718	0.0068	0.1001	16.2352	27.3955	-23.39
24	0.1658	-1.8551	0.3409	27.1118	-0.5609	2.3652	0.1151	0.4652	0.0049	-0.2059	-0.1568	0.0375	-0.0403	0.13	0.0417	0.159	0.003	0.0274	0.2816	-0.0222	0.0688	18.6964	35.3293	-20.5027
25	1.7299	0.3723	-2.289	0.8355	0.3755	4.2611	0.0374	0.0296	0.0946	-0.0758	-0.0357	0.2095	0.0067	0.095	-0.0017	0.1483	0.0055	-0.0085	0.2073	0.0332	0.1118	11.4659	48.0955	-15.8938
26	22.237	11.9228	12.5557	25.9957	7.6504	7.1324	0.042	-0.2296	0.0826	-0.1279	-0.5046	0.2096	0.1039	-0.3283	0.4626	0.1618	0.0141	0.0353	0.3504	-0.0503	-0.0456	-2.3825	46.7931	-2.0215
27	6.6401	-7.3698	-4.1586	9.3773	4.5193	2.8259	-0.2454	-0.149	-0.2988	0.2632	0.132	0.3536	0.1891	-0.0636	0.1134	0.1906	-0.042	-0.008	0.2069	0.0083	0.0758	3.7411	34.1103	-8.9428
28	2.4481	0.115	1.6163	14.3776	-1.8642	11.9713	-0.1647	0.13	-0.1736	0.0232	-0.0511	-0.6069	0.6653	0.7117	0.2159	0.3059	-0.029	-0.0298	0.1896	0.0172	0.0693	18.0399	20.902	-11.1992
29	0.482	1.7509	-0.2249	6.3643	-0.8399	0.2414	-0.0736	0.0762	0.0859	-0.019	0.169	0.0028	0.022	0.1376	-0.0954	0.2048	0.0092	-0.0124	0.2006	-0.013	0.0803	15.3919	38.8337	-8.4377
30	3.6514	-6.5905	0.6233	18.6433	-4.1501	2.1313	0.0661	0.1944	-0.0062	-0.2149	-0.1549	-0.3595	0.2259	0.4205	0.0888	0.1398	-0.0036	-0.009	0.2349	-0.015	0.0628	24.4405	39.5078	-11.1218

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	24 - 32	27 - 35
2	X-RAY DIFFRACTION	2	A	A	33 - 44	36 - 47
3	X-RAY DIFFRACTION	3	A	A	45 - 63	48 - 66
4	X-RAY DIFFRACTION	4	A	A	64 - 69	67 - 72
5	X-RAY DIFFRACTION	5	A	A	70 - 79	73 - 82
6	X-RAY DIFFRACTION	6	A	A	80 - 97	83 - 100
7	X-RAY DIFFRACTION	7	A	A	98 - 111	101 - 114
8	X-RAY DIFFRACTION	8	A	A	112 - 132	115 - 135
9	X-RAY DIFFRACTION	9	A	A	133 - 140	136 - 143
10	X-RAY DIFFRACTION	10	A	A	141 - 149	144 - 152
11	X-RAY DIFFRACTION	11	A	A	150 - 163	153 - 166
12	X-RAY DIFFRACTION	12	A	A	164 - 174	167 - 177
13	X-RAY DIFFRACTION	13	A	A	175 - 183	178 - 186
14	X-RAY DIFFRACTION	14	A	A	184 - 206	187 - 209
15	X-RAY DIFFRACTION	15	A	A	207 - 214	210 - 217
16	X-RAY DIFFRACTION	16	B	B	26 - 35	29 - 38
17	X-RAY DIFFRACTION	17	B	B	36 - 44	39 - 47
18	X-RAY DIFFRACTION	18	B	B	45 - 51	48 - 54
19	X-RAY DIFFRACTION	19	B	B	52 - 63	55 - 66
20	X-RAY DIFFRACTION	20	B	B	64 - 71	67 - 74
21	X-RAY DIFFRACTION	21	B	B	72 - 83	75 - 86
22	X-RAY DIFFRACTION	22	B	B	84 - 91	87 - 94
23	X-RAY DIFFRACTION	23	B	B	92 - 103	95 - 106
24	X-RAY DIFFRACTION	24	B	B	104 - 113	107 - 116
25	X-RAY DIFFRACTION	25	B	B	114 - 132	117 - 135
26	X-RAY DIFFRACTION	26	B	B	133 - 140	136 - 143
27	X-RAY DIFFRACTION	27	B	B	141 - 157	144 - 160
28	X-RAY DIFFRACTION	28	B	B	158 - 176	161 - 179
29	X-RAY DIFFRACTION	29	B	B	177 - 194	180 - 197
30	X-RAY DIFFRACTION	30	B	B	195 - 214	198 - 217

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