PDB-3tqn: Structure of the transcriptional regulator of the GntR family, fr...

ID or keywords:

Entry

Database: PDB / ID: 3tqn

Title

Structure of the transcriptional regulator of the GntR family, from Coxiella burnetii.

Components

Transcriptional regulator, GntR family

Keywords

TRANSCRIPTION / Regulatory functions

Function / homology

Function and homology information

DNA-binding transcription factor activity
Similarity search - Function

Biological species

Coxiella burnetii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.8 Å

Authors

Rudolph, M. / Cheung, J. / Franklin, M.C. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.

Citation

Journal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.

History

Deposition	Sep 9, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 28, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jun 24, 2015	Group: Database references
Revision 1.2	Jul 1, 2015	Group: Derived calculations
Revision 1.3	Oct 21, 2015	Group: Database references
Revision 1.4	Feb 10, 2016	Group: Database references
Revision 1.5	Nov 8, 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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PDBx/mmCIF format	3tqn.cif.gz	140.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3tqn.ent.gz	121.2 KB	Display	PDB format
PDBx/mmJSON format	3tqn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3tqn_validation.pdf.gz	444.2 KB	Display	wwPDB validaton report
Full document	3tqn_full_validation.pdf.gz	456.8 KB	Display
Data in XML	3tqn_validation.xml.gz	14.3 KB	Display
Data in CIF	3tqn_validation.cif.gz	18.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tq/3tqn ftp://data.pdbj.org/pub/pdb/validation_reports/tq/3tqn	HTTPS FTP

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Related structure data

Related structure data	3tq8C 3tq9C 3tqaC 3tqbC 3tqcC 3tqdC 3tqeC 3tqfC 3tqgC 3tqhC 3tqiC 3tqjC 3tqlC 3tqmC 3tqoC 3tqpC 3tqqC 3tqrC 3tqsC 3tqtC 3tquC 3tqwC 3tqxC 3tqyC 3tqzC 3tr0C 3tr1C 3tr2C 3tr3C 3tr4C 3tr5C 3tr6C 3tr7C 3tr8C 3tr9C 3trbC 3trcC 3trdC 3treC 3trfC 3trgC 3trhC 3triC 3tthC 3ty2C 3uwcC 4f3qC 4f3rC 4nbqC 4ng4C C: citing same article (ref.)
Similar structure data	2zhh-1 6ekq-d 5kj4-4 5ulh-d 6pln-d 1ge9-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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Transcriptional regulator, GntR family

B: Transcriptional regulator, GntR family

C: Transcriptional regulator, GntR family

40.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Transcriptional regulator, GntR family

C: Transcriptional regulator, GntR family

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

2

B: Transcriptional regulator, GntR family

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

Unit cell

Length a, b, c (Å)	68.057, 68.057, 194.466
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	Transcriptional regulator, GntR family Mass: 13544.280 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA493 / Gene: CBU_0775 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83DG1

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.77 Å³/Da / Density % sol: 55.61 %
Crystal grow	Temperature: 293 K / pH: 4 Details: 100 mM Trisodium Citrate 20% PEG 6000, pH 4.0, sitting drop, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X4C / Wavelength: 0.979 Å

Detector

Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 28, 2011

Radiation

Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 2.7→50 Å / Num. all: 13383 / Num. obs: 13383 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 20.6 % / R_merge(I) obs: 0.074 / Χ²: 1.307 / Net I/σ(I): 13.9

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.7-2.75	13.3	0.762	664	0.893	1	100
2.75-2.8	14	0.538	622	0.796	1	100
2.8-2.85	14.3	0.477	667	0.807	1	100
2.85-2.91	14.6	0.358	640	0.789	1	100
2.91-2.97	14.3	0.303	659	0.803	1	100
2.97-3.04	14.5	0.228	643	0.817	1	100
3.04-3.12	14.3	0.17	657	0.849	1	100
3.12-3.2	14.5	0.163	643	0.971	1	100
3.2-3.3	14.4	0.123	663	1.015	1	100
3.3-3.4	14.3	0.104	661	1.063	1	100
3.4-3.52	22.8	0.197	646	1.361	1	100
3.52-3.66	28.5	0.175	665	1.317	1	100
3.66-3.83	28.4	0.119	668	1.46	1	100
3.83-4.03	28	0.086	676	1.532	1	100
4.03-4.29	28.3	0.064	658	1.602	1	100
4.29-4.62	28	0.063	683	1.743	1	100
4.62-5.08	27.6	0.056	675	1.62	1	100
5.08-5.81	27.3	0.061	690	1.747	1	100
5.81-7.32	26.6	0.064	710	1.422	1	100
7.32-50	21	0.039	793	1.301	1	99.6

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
PHENIX	1.6.4_486	refinement
PDB_EXTRACT	3.1	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.8→46.938 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7478 / SU ML: 0.4 / σ(F): 0 / Phase error: 30.1 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2963	572	4.79 %
R_work	0.2621	11365	-
obs	0.2638	11937	99.81 %

Solvent computation

Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 55.83 Å² / k_sol: 0.324 e/Å³

Displacement parameters

B_iso max: 423.38 Å² / B_iso mean: 87.8199 Å² / B_iso min: 18.39 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.7278 Å²	-0 Å²	-0 Å²
2-	-	1.7278 Å²	-0 Å²
3-	-	-	-3.4555 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→46.938 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2588	0	0	0	2588

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	2623
X-RAY DIFFRACTION	f_angle_d	1.091	3513
X-RAY DIFFRACTION	f_chiral_restr	0.077	389
X-RAY DIFFRACTION	f_plane_restr	0.003	441
X-RAY DIFFRACTION	f_dihedral_angle_d	20.289	1060

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.8-3.082	0.4528	135	0.3548	2774	2909	100
3.082-3.5279	0.3376	142	0.2982	2778	2920	100
3.5279-4.4442	0.2829	150	0.2436	2801	2951	99
4.4442-46.9446	0.2625	145	0.2437	3012	3157	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	6.777	0.1777	-0.8687	0.011	-0.1328	1.4108	0.0468	0.4588	0.6323	-0.166	-0.6093	-0.5998	0.2857	0.0881	0.5838	0.5102	-0.0679	0.1782	0.6057	-0.049	0.921	25.3283	39.8063	68.0117
2	3.5451	-1.1546	-0.3995	1.9129	-1.6045	3.4982	0.2265	-0.0266	0.1265	-0.2504	-0.0747	0.131	0.3469	0.2886	-0.0793	0.3279	0.051	-0.0106	0.1908	-0.0655	0.2774	23.9752	40.5857	79.2453
3	1.4844	1.0232	0.5151	0.8943	1.3365	5.1227	-0.0969	-0.3802	0.6774	-0.1719	0.0402	0.0761	-0.7205	0.2917	0.073	0.2876	-0.0966	0.0156	0.224	-0.0974	0.4952	23.0927	50.6803	87.5769
4	1.2815	0.093	0.484	1.2868	-1.4314	3.4762	-0.0119	-0.1276	0.5653	0.2679	-0.2354	0.1433	-0.407	-0.0479	0.1767	0.1732	-0.1711	0.0256	-0.5989	-0.0239	0.4235	15.5536	46.9439	78.8229
5	0.1781	0.0544	0.3058	0.0201	0.1032	0.5145	-0.2332	-0.1505	0.1298	0.6792	-0.2233	0.0662	0.188	-0.2136	0.3682	0.5323	-0.1083	0.0873	-0.0174	-0.4273	0.2655	15.1869	50.0463	90.5761
6	1.9439	-0.7483	-0.3912	0.3474	0.5721	3.0476	-0.0967	-0.0495	-0.3268	0.8954	0.0024	0.1111	0.8241	0.0439	0.1174	0.7023	0.0161	-0.0322	0.2218	0.0557	0.4383	24.5856	30.5909	87.7574
7	1.2594	0.0476	0.3941	4.3868	-1.0257	0.3666	-0.0298	0.2254	-0.0853	0.3554	0.3461	0.3	0.3646	0.2896	-0.2442	0.8287	0.1709	-0.1104	0.5553	-0.0751	0.5956	32.3431	14.5014	78.5024
8	0.0404	0.3681	0.0214	3.0904	0.2291	0.0148	0.0035	-0.3157	-0.0141	0.16	0.4713	-1.1305	0.017	0.4008	-0.4085	0.5929	0.3878	0.0758	0.705	0.0106	0.8012	42.508	46.5563	83.4702
9	0.8363	0.1802	0.634	1.8646	0.8459	1.853	0.1463	0.0972	0.0551	0.0927	0.0302	-0.4474	-0.0809	0.3744	-0.1035	-0.3189	0.1419	-0.4643	0.0554	0.147	-0.2353	41.373	56.8992	83.6788
10	0.4634	0.8654	-0.5007	8.8435	-1.7686	0.6409	0.0293	0.2013	0.168	-1.0344	0.1248	0.408	0.1866	0.0342	-0.0163	0.39	0.0656	-0.0761	0.2566	-0.0931	-0.2182	39.7083	65.5831	73.6045
11	2.6542	0.871	1.739	3.6806	1.0643	1.2045	-0.0748	0.4462	-0.0511	-0.9071	0.147	0.1885	-0.0688	0.3576	-0.1023	0.2875	0.0432	-0.0465	0.5876	-0.1507	0.0651	35.3627	50.282	72.2447
12	0.0117	-0.2108	0.0812	4.3009	0.3281	1.3305	0.0124	0.0256	-0.0299	0.0536	-0.1506	1.1082	-0.1043	-0.3905	0.0627	0.0987	0.0522	-0.0207	0.2606	-0.0165	0.3417	30.7964	60.5333	81.1895
13	1.8426	-0.2428	1.3912	1.323	-0.4464	3.5569	-0.038	-0.3334	-0.1071	-0.0015	-0.0378	0.3418	-0.5527	-0.0997	0.1778	0.5382	0.0263	-0.1557	0.2092	0.2149	0.0408	40.6496	66.4143	86.787
14	2.2882	0.0253	-0.3236	1.434	2.5647	4.6478	0.2145	-0.5221	0.0879	0.7694	0.1437	0.0848	1.0891	-0.377	-0.281	0.6161	-0.1012	-0.0762	0.3584	0.0854	0.3656	59.7518	57.1153	102.9762
15	2.2962	-1.6965	-1.4065	4.7159	-0.2151	6.217	-0.1069	-0.0997	0.2035	0.6888	-0.0017	-0.0934	-0.9656	-0.4059	0.0882	1.2065	0.0999	0.0135	0.9342	-0.0348	0.9942	32.6281	22.8212	54.5577
16	0.6784	0.4569	-0.1376	1.7504	-0.2069	1.3085	-0.0478	-0.0383	-0.0598	0.4398	0.0687	-0.2076	-0.4092	-0.1703	-0.0053	0.8316	0.3112	-0.6349	0.4023	0.2591	0.3167	32.6434	13.2329	59.5511
17	8.088	-2.4108	2.6697	4.9326	0.2457	3.4588	0.3188	1.2241	-0.1611	-0.1479	-0.353	-0.1161	-0.1413	-0.0948	0.1381	0.6339	0.1222	-0.1302	0.8281	-0.117	0.3824	30.4922	1.7869	56.904
18	0.8492	-0.4172	-0.1717	0.3486	-0.0856	0.2378	0.0292	0.7275	0.1627	-0.1826	-0.3103	-0.0886	-0.5219	0.3163	0.3442	1.0323	0.3542	-0.2603	1.0896	0.0604	0.543	26.6015	13.7028	46.9344
19	0.502	0.0015	-0.342	1.7031	-1.3262	1.2656	0.0291	0.6043	0.2129	-0.3362	-0.451	-0.2462	-0.6036	0.5511	0.474	0.7885	-0.1396	-0.0969	1.339	0.2032	0.5556	39.554	10.6732	50.9027
20	0.7047	1.6177	-3.0111	3.6816	-6.8568	2.0015	0.0124	0.7733	0.3707	-0.2222	0.2505	0.1284	0.9598	0.3678	-0.2893	0.7437	0.1513	-0.2607	0.8914	0.0519	0.3958	39.06	2.5528	52.9598
21	2.1107	2.7009	1.2016	5.353	-1.0615	4.1716	0.2037	0.3734	-0.1813	0.4266	0.1791	-0.2825	-0.0565	0.6971	-0.3396	0.3681	0.0448	-0.0584	0.6114	-0.0493	0.5245	41.509	12.9037	68.6872
22	0.0038	0.0387	0.2044	0.2695	1.4035	7.3305	0.1062	-0.2726	0.3655	0.402	-0.1915	0.185	-1.2653	0.265	0.0431	1.478	-0.1505	0.0896	0.4525	0.0786	0.7511	38.72	24.7123	79.034
23	2.0061	6.8944	-1.8874	2.0006	4.738	1.998	-0.6414	-0.8016	0.4896	-1.9428	0.3407	0.5418	0.0074	-0.1756	0.308	0.7186	-0.2327	-0.1354	0.7829	-0.1256	0.8445	34.5208	24.633	88.9804

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain A and (resseq 1:9)	A	1 - 9
2	X-RAY DIFFRACTION	2	chain A and (resseq 10:24)	A	10 - 24
3	X-RAY DIFFRACTION	3	chain A and (resseq 25:35)	A	25 - 35
4	X-RAY DIFFRACTION	4	chain A and (resseq 36:66)	A	36 - 66
5	X-RAY DIFFRACTION	5	chain A and (resseq 67:76)	A	67 - 76
6	X-RAY DIFFRACTION	6	chain A and (resseq 77:92)	A	77 - 92
7	X-RAY DIFFRACTION	7	chain A and (resseq 93:107)	A	93 - 107
8	X-RAY DIFFRACTION	8	chain B and (resseq 1:9)	B	1 - 9
9	X-RAY DIFFRACTION	9	chain B and (resseq 10:24)	B	10 - 24
10	X-RAY DIFFRACTION	10	chain B and (resseq 25:35)	B	25 - 35
11	X-RAY DIFFRACTION	11	chain B and (resseq 36:46)	B	36 - 46
12	X-RAY DIFFRACTION	12	chain B and (resseq 47:66)	B	47 - 66
13	X-RAY DIFFRACTION	13	chain B and (resseq 67:92)	B	67 - 92
14	X-RAY DIFFRACTION	14	chain B and (resseq 93:108)	B	93 - 108
15	X-RAY DIFFRACTION	15	chain C and (resseq 7:11)	C	7 - 11
16	X-RAY DIFFRACTION	16	chain C and (resseq 12:23)	C	12 - 23
17	X-RAY DIFFRACTION	17	chain C and (resseq 24:35)	C	24 - 35
18	X-RAY DIFFRACTION	18	chain C and (resseq 36:53)	C	36 - 53
19	X-RAY DIFFRACTION	19	chain C and (resseq 54:59)	C	54 - 59
20	X-RAY DIFFRACTION	20	chain C and (resseq 60:76)	C	60 - 76
21	X-RAY DIFFRACTION	21	chain C and (resseq 77:92)	C	77 - 92
22	X-RAY DIFFRACTION	22	chain C and (resseq 93:100)	C	93 - 100
23	X-RAY DIFFRACTION	23	chain C and (resseq 101:109)	C	101 - 109

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