PDB-5bs6: Apo structure of transcriptional factor AraR from Bacteroides the...

ID or keywords:

Entry

Database: PDB / ID: 5bs6

Title

Apo structure of transcriptional factor AraR from Bacteroides thetaiotaomicron VPI

Components

transcriptional regulator AraR

Keywords

TRANSCRIPTION / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / transcriptional regulator / Bacteroides thetaiotaomicron / helix-turn-helix motif / Nudix fold / DNA binding

Function / homology

Function and homology information

hydrolase activity / DNA binding
Similarity search - Function

Biological species

Bacteroides thetaiotaomicron (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.35 Å

Authors

Chang, C. / Tesar, C. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: Nucleic Acids Res. / Year: 2015
Title: A novel transcriptional regulator of L-arabinose utilization in human gut bacteria.
Authors: Chang, C. / Tesar, C. / Li, X. / Kim, Y. / Rodionov, D.A. / Joachimiak, A.

History

Deposition	Jun 1, 2015	Deposition site: RCSB / Processing site: RCSB
Supersession	Jun 17, 2015	ID: 2FB1
Revision 1.0	Jun 17, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jun 24, 2015	Group: Other
Revision 1.2	Oct 21, 2015	Group: Database references
Revision 1.3	Dec 16, 2015	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5bs6.cif.gz	365.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5bs6.ent.gz	315.1 KB	Display	PDB format
PDBx/mmJSON format	5bs6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5bs6_validation.pdf.gz	460.5 KB	Display	wwPDB validaton report
Full document	5bs6_full_validation.pdf.gz	466.2 KB	Display
Data in XML	5bs6_validation.xml.gz	34.1 KB	Display
Data in CIF	5bs6_validation.cif.gz	48.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bs/5bs6 ftp://data.pdbj.org/pub/pdb/validation_reports/bs/5bs6	HTTPS FTP

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Related structure data

Related structure data	5dd4C 5ddgC 5deqC C: citing same article (ref.)
Similar structure data	2o0y-2 7bxf-d 5yk3-1 3uug-d 5dd4-1 5kgj-1 6der-d 6den-d 5ojo-d 6deq-d 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
Other databases	TargetTrack: MCSG-APC111381 TargetTrack: MCSG-APC81302

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#145 - Jan 2012 Messenger RNA Capping similarity (4) #201 - Sep 2016 Isoprene Synthase similarity (4)

Deposited unit

A: transcriptional regulator AraR

B: transcriptional regulator AraR

C: transcriptional regulator AraR

D: transcriptional regulator AraR

hetero molecules

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

1

A: transcriptional regulator AraR

B: transcriptional regulator AraR

hetero molecules

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

2

C: transcriptional regulator AraR

D: transcriptional regulator AraR

hetero molecules

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

Unit cell

Length a, b, c (Å)	176.437, 176.437, 118.426
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	146
Space group name H-M	H3

#1: Protein	transcriptional regulator AraR Mass: 26622.131 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria) Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_0354 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8AAV8
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 259 / 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: 3.42 Å³/Da / Density % sol: 64.07 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 0.4 M sodium di-hydrogen phosphate/1.6M di-potassium hydrogen phosphate, 0.2 M sodum chloride, 0.1 M Tris

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.9794 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2005

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9794 Å / Relative weight: 1

Reflection

Resolution: 2.35→50 Å / Num. obs: 56682 / % possible obs: 99.7 % / Redundancy: 3.7 % / R_merge(I) obs: 0.117 / Χ²: 0.875 / Net I/av σ(I): 12.308 / Net I/σ(I): 9.6 / Num. measured all: 211562

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	% possible all
2.35-2.39	3.4	0.831	2767	0.964	98.1
2.39-2.43	3.5	0.864	2817	1.003	98.5
2.43-2.48	3.6	0.825	2819	0.982	98.9
2.48-2.53	3.6	0.716	2791	0.98	99
2.53-2.59	3.7	0.623	2872	0.982	99.5
2.59-2.65	3.7	0.565	2817	0.982	99.9
2.65-2.71	3.7	0.438	2829	0.934	99.9
2.71-2.79	3.7	0.36	2865	0.956	100
2.79-2.87	3.8	0.279	2842	0.905	100
2.87-2.96	3.8	0.219	2816	0.873	100
2.96-3.07	3.8	0.172	2857	0.843	100
3.07-3.19	3.8	0.137	2836	0.81	100
3.19-3.33	3.9	0.108	2836	0.749	100
3.33-3.51	3.8	0.086	2873	0.709	100
3.51-3.73	3.8	0.072	2844	0.671	100
3.73-4.02	3.8	0.067	2840	0.632	100
4.02-4.42	3.8	0.066	2851	0.629	100
4.42-5.06	3.8	0.064	2844	0.627	100
5.06-6.37	3.7	0.069	2847	0.67	99.8
6.37-50	3.9	0.116	2819	1.67	99.5

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
REFMAC	5.7.0029	refinement
PDB_EXTRACT	3.15	data extraction
HKL-2000		data reduction
HKL-3000		phasing
SBC-Collect		data collection

Refinement

Method to determine structure:

SAD / Resolution: 2.35→41.38 Å / Cor.coef. F_o:F_c: 0.938 / Cor.coef. F_o:F_c free: 0.913 / SU B: 12.579 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.299 / ESU R Free: 0.224
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.233	2641	5.1 %	RANDOM
R_work	0.1954	-	-	-
obs	0.1973	49428	91.31 %	-

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 max: 135.19 Å² / B_iso mean: 38.864 Å² / B_iso min: 7.43 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.57 Å²	-0.57 Å²	-0 Å²
2-	-	-0.57 Å²	0 Å²
3-	-	-	1.86 Å²

Refinement step

Cycle: final / Resolution: 2.35→41.38 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7213	0	16	259	7488
B_iso mean	-	-	28.59	31.31	-
Num. residues	-	-	-	-	902

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	7380
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	7032
X-RAY DIFFRACTION	r_angle_refined_deg	1.231	1.987	9938
X-RAY DIFFRACTION	r_angle_other_deg	0.685	3	16171
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.918	5	897
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.052	24.46	361
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.707	15	1203
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.975	15	42
X-RAY DIFFRACTION	r_chiral_restr	0.067	0.2	1049
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	8361
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1709

LS refinement shell

Resolution: 2.354→2.415 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.285	74	-
R_work	0.245	1599	-
all	-	1673	-
obs	-	-	39.38 %

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	12.1633	-5.0967	4.6933	19.7225	2.6343	3.0147	0.1119	-0.1623	0.6701	0.1846	-0.0876	-1.3354	0.1107	-0.0991	-0.0243	0.1956	0.0135	-0.0426	0.2718	-0.0964	0.2003	119.7201	18.906	22.4976
2	0.2191	0.2131	0.2875	0.7492	0.3419	1.4717	-0.0276	0.0578	0.056	0.0066	0.0897	-0.0502	-0.0194	0.0272	-0.0621	0.2579	0.0043	0.0024	0.2308	-0.0408	0.1607	109.7744	4.833	-1.8913
3	0.5299	0.5663	0.6293	1.6645	-0.0651	1.2755	0.0387	0.0488	-0.0265	-0.0748	0.1108	0.1953	0.1452	0.0007	-0.1495	0.2386	0.0398	0.0128	0.2257	-0.0509	0.1419	104.7532	-0.2874	-7.7065
4	0.1822	-0.0319	0.9995	0.0622	-0.274	5.6732	-0.1153	0.002	0.0199	-0.0267	0.1298	0.0422	-0.5688	-0.2181	-0.0145	0.3076	-0.0245	-0.0317	0.3293	0.1106	0.157	98.7468	14.4988	-18.6383
5	2.3967	0.7817	1.3828	0.3727	0.0794	3.1626	-0.0875	-0.0582	0.2489	-0.0743	0.0909	0.2139	-0.3228	-0.0702	-0.0034	0.2609	-0.0127	-0.0951	0.2243	0.1963	0.2488	95.0691	15.0784	-28.7691
6	0.1765	0.1076	0.9192	3.0015	5.1083	12.1034	-0.1233	0.0528	0.0682	-0.1243	0.0904	-0.1088	-0.825	0.1313	0.0329	0.3954	-0.0291	-0.0468	0.2095	0.1127	0.2051	101.847	22.7051	-23.7093
7	0.3399	-0.2878	0.0405	1.1783	0.3112	0.1637	-0.0152	0.0026	0.018	0.0765	0.0832	-0.0898	0.0024	-0.0249	-0.068	0.2724	0.0103	0.0218	0.2242	-0.0416	0.1808	107.3143	20.0335	15.0678
8	1.4222	-0.0893	-0.3344	2.2226	0.1314	0.7528	0.0039	0.0503	0.1833	0.1467	-0.0491	-0.0124	-0.1563	-0.0225	0.0452	0.27	0.0348	0.012	0.189	-0.069	0.1017	102.1701	31.738	16.8892
9	3.3216	-3.8511	-1.9141	4.4862	1.9616	4.3687	0.4984	0.4613	-0.2134	-0.5357	-0.5043	0.2548	-0.1905	-0.0884	0.0059	0.2876	0.0517	-0.0314	0.2858	-0.0708	0.1587	93.7146	26.2524	1.8691
10	2.4642	0.046	0.7192	2.6857	-0.4458	0.3259	-0.0046	0.286	0.1068	-0.1039	-0.0289	0.1087	0.0823	0.0281	0.0336	0.2339	0.0262	0.0056	0.3099	0.0108	0.2193	83.7433	34.767	6.7206
11	3.5601	-1.0529	0.6788	1.4966	1.6693	3.1093	-0.0372	0.1152	-0.0682	-0.0938	0.0898	0.0276	-0.2191	0.1782	-0.0526	0.187	0.0249	-0.0075	0.2615	0.0065	0.201	74.0207	34.0153	9.3669
12	1.9841	-2.8198	-1.5805	4.9666	3.5463	3.1279	-0.0909	0.0863	-0.278	0.2729	-0.0919	0.4208	0.2245	-0.1847	0.1828	0.174	0.0199	0.0042	0.3053	-0.0242	0.3109	77.015	29.3116	10.6195
13	2.4252	-0.8696	0.1405	0.3261	-0.0518	0.0206	-0.067	-0.4313	0.2024	-0.0172	0.1105	-0.0724	0.01	-0.015	-0.0435	0.3128	0.0551	-0.0102	0.2511	-0.0799	0.2671	101.7656	-19.9337	-20.8762
14	0.3933	-0.9797	0.3882	3.3227	-0.7403	0.5358	-0.0669	-0.015	0.032	0.0077	0.0455	-0.2732	-0.0134	-0.0909	0.0214	0.2606	0.0418	0.0016	0.2381	-0.0135	0.2	113.8361	-47.9568	-27.2631
15	0.4413	0.0164	-0.3351	1.5729	-0.0676	0.8923	0.0205	-0.0354	-0.0549	-0.0439	-0.0439	-0.0784	-0.0422	-0.068	0.0234	0.2511	0.0179	0.004	0.2345	-0.0316	0.1574	110.3579	-50.6661	-29.1656
16	0.2903	-0.5699	0.1475	2.0372	-0.8731	1.1479	-0.0627	-0.0198	-0.0246	0.0476	-0.1015	-0.2816	0.046	-0.0191	0.1642	0.1867	-0.0048	0.0034	0.2078	-0.0283	0.1991	120.3389	-58.8756	-23.405
17	2.4617	4.6011	0.6747	11.2639	0.4637	1.1475	0.3803	-0.2387	0.2633	-0.043	-0.5658	-0.927	0.4128	0.9895	0.1855	0.3612	0.1058	0.302	1.462	-0.3931	0.9781	133.3775	-67.9697	-12.5783
18	0.593	0.9205	0.7632	6.7995	0.9759	1.0035	-0.0668	-0.047	-0.0018	0.2902	0.0421	0.1808	-0.0859	-0.0406	0.0248	0.2647	0.0286	-0.0355	0.2666	0.0185	0.1431	119.7733	-70.3993	-6.8929
19	6.6322	4.935	-11.1809	7.8349	-5.3002	21.0551	-0.295	-0.017	-0.1693	-0.3255	-0.2147	0.1891	0.3726	-0.1761	0.5098	0.2476	0.0773	-0.0786	0.2958	0.0488	0.0853	106.2006	-39.7352	-46.656
20	0.5583	0.0927	-0.6029	0.2	-0.2157	0.7853	0.0757	0.0491	0.1051	-0.0803	-0.1073	-0.0616	-0.0674	-0.0762	0.0316	0.2695	0.076	-0.04	0.2701	-0.073	0.1926	106.8259	-34.1366	-28.3184
21	9.0107	-0.4961	8.4184	1.8024	2.5161	12.8809	0.0248	-0.1775	0.2001	0.0621	0.0702	-0.1719	0.1923	-0.0545	-0.095	0.2416	0.043	-0.0648	0.241	-0.0846	0.2091	126.556	-27.6258	-4.1064
22	0.961	0.1791	0.0289	1.0614	0.8935	1.0223	0.0099	-0.0186	-0.0128	-0.0287	0.0157	-0.0829	-0.0136	0.0117	-0.0256	0.2388	0.0188	-0.0255	0.2089	-0.0599	0.1723	116.6482	-26.2541	-13.8493
23	3.0857	1.1099	2.4774	1.0995	0.8633	2.0033	0.1284	0.1424	-0.5112	0.0364	0.2168	-0.2452	0.0762	0.1367	-0.3453	0.1178	0.0515	-0.1093	0.2618	-0.0521	0.3788	134.3627	-34.843	-4.309
24	3.9238	2.2453	1.7508	1.9256	1.2698	0.9227	-0.152	0.1665	-0.7042	0.0273	0.353	-0.1685	-0.0712	0.2334	-0.201	0.1647	0.0299	-0.0559	0.3305	-0.0767	0.4277	145.1276	-32.9512	-4.0705

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 7
2	X-RAY DIFFRACTION	2	A	8 - 104
3	X-RAY DIFFRACTION	3	A	105 - 140
4	X-RAY DIFFRACTION	4	A	141 - 171
5	X-RAY DIFFRACTION	5	A	172 - 205
6	X-RAY DIFFRACTION	6	A	206 - 225
7	X-RAY DIFFRACTION	7	B	0 - 99
8	X-RAY DIFFRACTION	8	B	100 - 138
9	X-RAY DIFFRACTION	9	B	139 - 149
10	X-RAY DIFFRACTION	10	B	150 - 182
11	X-RAY DIFFRACTION	11	B	183 - 202
12	X-RAY DIFFRACTION	12	B	203 - 225
13	X-RAY DIFFRACTION	13	C	0 - 5
14	X-RAY DIFFRACTION	14	C	6 - 27
15	X-RAY DIFFRACTION	15	C	28 - 110
16	X-RAY DIFFRACTION	16	C	111 - 172
17	X-RAY DIFFRACTION	17	C	173 - 183
18	X-RAY DIFFRACTION	18	C	184 - 225
19	X-RAY DIFFRACTION	19	D	0 - 4
20	X-RAY DIFFRACTION	20	D	5 - 17
21	X-RAY DIFFRACTION	21	D	18 - 27
22	X-RAY DIFFRACTION	22	D	28 - 140
23	X-RAY DIFFRACTION	23	D	141 - 178
24	X-RAY DIFFRACTION	24	D	179 - 225

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