PDB-6f7f: Tryptophan Repressor TrpR from E.coli with 3-Indolepropionic acid

ID or keywords:

Entry

Database: PDB / ID: 6f7f

Title

Tryptophan Repressor TrpR from E.coli with 3-Indolepropionic acid

Components

Trp operon repressor

Keywords

TRANSCRIPTION /

Ligand Binding

Function / homology

Function and homology information

sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription /

DNA binding /

cytoplasm
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.128 Å

Authors

Stiel, A.C. / Shanmugaratnam, S. / Hocker, B.

Funding support

Germany, 1items

Citation

Journal: To Be Published
Title: Tryptophan Repressor TrpR: A study of ligand binding specificity
Authors: Stiel, A.C. / Shanmugaratnam, S. / Hocker, B.

History

Deposition	Dec 8, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 27, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6f7f.cif.gz	186.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6f7f.ent.gz	149.6 KB	Display	PDB format
PDBx/mmJSON format	6f7f.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/f7/6f7f ftp://data.pdbj.org/pub/pdb/validation_reports/f7/6f7f	HTTPS FTP

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Related structure data

Related structure data	1troS S: Starting model for refinement
Similar structure data	1zt9-1 1zt9-2 6ejz-2 6ejw-2 3n4s-2 6ejw-1 4nxb-d 2dx0-d 6ejz-1 2pze-1 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
Related items in Molecule of the Month	#168 - Dec 2013 DNA Helicase similarity (1)

Deposited unit

B: Trp operon repressor

A: Trp operon repressor

D: Trp operon repressor

C: Trp operon repressor

hetero molecules

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

1

B: Trp operon repressor

A: Trp operon repressor

hetero molecules

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

2

D: Trp operon repressor

C: Trp operon repressor

hetero molecules

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

Unit cell

Length a, b, c (Å)	81.840, 81.840, 70.570
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	78
Space group name H-M	P4₃

#1: Protein	Trp operon repressor Mass: 11837.562 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trpR, rtrY, b4393, JW4356 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A881
#2: Chemical	ChemComp-IOP / INDOLYLPROPIONIC ACID / 3-Indolepropionic acid Mass: 189.211 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₁H₁₁NO₂
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.5 Å³/Da / Density % sol: 50.71 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M Calcium Chloride 0.1 M HEPES pH7.5 30% PEG 4000

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X10SA / Wavelength: 0.99999 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2015

Radiation

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

Radiation wavelength

Wavelength: 0.99999 Å / Relative weight: 1

Reflection

Resolution: 2.128→44.748 Å / Num. obs: 26153 / % possible obs: 99.5 % / Redundancy: 12.331 % / B_iso Wilson estimate: 26.77 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.18 / R_rim(I) all: 0.188 / Χ²: 0.93 / Net I/σ(I): 12.2

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.128-2.18	8.164	1.014	2.47	1828	0.716	1.079	93.9
2.18-2.24	12.133	0.913	3.72	1864	0.85	0.953	100
2.24-2.31	12.813	0.763	4.66	1843	0.917	0.795	100
2.31-2.38	12.89	0.662	5.39	1768	0.943	0.69	100
2.38-2.46	12.946	0.536	6.79	1750	0.959	0.558	100
2.46-2.54	12.851	0.487	7.43	1657	0.97	0.508	100
2.54-2.64	12.771	0.415	8.89	1626	0.98	0.432	100
2.64-2.75	11.968	0.353	9.77	1533	0.982	0.369	100
2.75-2.87	11.946	0.331	10.8	1469	0.984	0.346	100
2.87-3.01	13.337	0.281	12.54	1456	0.989	0.293	100
3.01-3.17	13.305	0.212	15.2	1349	0.992	0.22	100
3.17-3.36	13.158	0.16	18.16	1282	0.994	0.166	100
3.36-3.6	12.85	0.131	20.43	1214	0.996	0.136	100
3.6-3.89	12.105	0.119	21.65	1129	0.995	0.124	100
3.89-4.26	11.431	0.098	22.57	1038	0.995	0.103	100
4.26-4.76	13.087	0.095	25.23	926	0.996	0.099	100
4.76-5.49	13.151	0.092	24.92	848	0.997	0.095	100
5.49-6.73	12.627	0.099	23.16	711	0.997	0.103	100
6.73-9.52	11.431	0.085	25.87	547	0.997	0.089	100
9.52-44.748	12.927	0.076	32.26	315	0.998	0.079	99.1

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	2.13 Å	44.75 Å
Translation	2.13 Å	44.75 Å

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Processing

Software

Name	Version	Classification
PHENIX		refinement
XDS		data reduction
XSCALE		data scaling
PHASER	2.5.6	phasing
PDB_EXTRACT	3.24	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1tro

1tro

Resolution: 2.128→44.748 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.84

	R_factor	Num. reflection	% reflection
R_free	0.2292	1308	5 %
R_work	0.1718	-	-
obs	0.1747	26149	99.54 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 112.96 Å² / B_iso mean: 36.0904 Å² / B_iso min: 15.17 Å²

Refinement step

Cycle: final / Resolution: 2.128→44.748 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3284	0	56	324	3664
B_iso mean	-	-	30.3	37.59	-
Num. residues	-	-	-	-	408

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	3416
X-RAY DIFFRACTION	f_angle_d	0.428	4616
X-RAY DIFFRACTION	f_chiral_restr	0.031	514
X-RAY DIFFRACTION	f_plane_restr	0.003	600
X-RAY DIFFRACTION	f_dihedral_angle_d	7.456	2512

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 9

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.1281-2.2133	0.3229	140	0.2541	2663	2803	96
2.2133-2.314	0.2706	144	0.1989	2741	2885	100
2.314-2.436	0.2565	145	0.1887	2757	2902	100
2.436-2.5886	0.2446	146	0.1806	2757	2903	100
2.5886-2.7884	0.2779	144	0.1802	2754	2898	100
2.7884-3.069	0.2427	147	0.1858	2781	2928	100
3.069-3.5129	0.2239	146	0.1616	2771	2917	100
3.5129-4.4253	0.1989	146	0.1463	2779	2925	100
4.4253-44.7579	0.1912	150	0.1598	2838	2988	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	4.6041	5.8699	1.4245	7.6097	1.7362	1.8529	0.0254	-0.5492	-0.2275	-0.2488	-0.402	-0.16	0.0492	0.0877	0.3007	0.2066	0.0588	0.0046	0.2429	0.0709	0.2644	135.4163	101.1269	27.302
2	2.1927	1.0803	-1.7129	2.8682	-3.3247	6.1112	-0.1254	0.2001	0.0306	-0.0275	0.0599	-0.0195	0.1347	-0.5401	0.0479	0.1804	-0.0334	-0.007	0.1604	-0.0152	0.2606	120.5781	102.5469	17.6916
3	7.7023	-2.321	-3.1764	7.1236	2.1339	7.5801	-0.209	1.2056	0.3128	-1.6951	0.077	1.1855	-0.7526	-0.5923	0.1716	0.5539	-0.0544	-0.1169	0.5483	0.0474	0.4905	118.1382	111.7299	0.8022
4	5.9993	-5.3609	-1.5216	9.6239	2.5798	4.7097	-0.0801	-0.0384	-0.4789	0.1122	-0.1811	0.0404	0.1201	-0.0715	0.2007	0.1738	-0.0524	0.0548	0.2017	-0.0239	0.2354	129.2188	111.8865	6.5068
5	4.9188	-1.3628	-0.8956	7.032	2.5152	6.2025	-0.6072	0.7138	-0.7014	-1.0084	0.5232	-0.4992	0.9732	0.1762	-0.0093	0.5164	-0.049	0.1173	0.2317	-0.0312	0.3258	129.831	95.3981	4.9357
6	7.2204	-1.2552	1.3245	0.4037	0.4616	2.3837	-0.0163	0.0726	0.0698	-0.097	-0.1821	-0.0057	0.0778	-0.2416	0.1613	0.2409	-0.0496	0.0178	0.1757	-0.0466	0.2286	115.4746	100.2701	15.8596
7	1.6361	0.7825	-1.7927	1.9839	2.3305	8.1205	0.149	-0.1413	-0.0989	-0.0282	0.0069	-0.1638	-0.0134	0.2512	-0.1724	0.1378	0.0531	-0.011	0.1852	0.028	0.2774	130.8588	104.1182	25.4616
8	2.0219	2.8755	-2.7604	5.2957	-5.429	6.2316	-0.213	-1.1042	0.5954	1.8364	0.289	-0.936	-0.9587	0.0488	-0.0089	0.5529	0.0646	-0.0759	0.5634	-0.0977	0.5519	130.374	113.7335	42.193
9	6.3406	0.5732	-0.5331	4.8936	0.0677	2.6246	-0.0323	-0.4595	-0.5085	0.2336	-0.01	0.147	0.3609	-0.1348	0.0649	0.2418	-0.0117	0.0374	0.3011	0.0367	0.176	121.769	101.3872	37.5507
10	8.2249	3.9995	2.5272	5.6886	4.2844	4.1077	0.0133	-1.0691	0.9013	1.7518	0.4002	-0.0308	0.5778	-0.7598	-0.341	0.4005	0.0817	-0.0842	0.5717	-0.1767	0.3884	81.3306	101.5839	9.4387
11	5.5193	-4.8709	-0.52	6.0114	0.8593	2.0271	-0.0864	-0.0863	0.1307	-0.1363	0.0255	0.087	-0.2773	0.0798	0.0182	0.2441	-0.056	-0.0424	0.2192	-0.0095	0.2349	100.7283	98.4965	8.0019
12	2.7976	0.6379	1.6488	1.8849	-1.7226	5.4419	0.0063	0.0104	-0.108	-0.132	0.105	-0.0794	0.2775	-0.0477	-0.1469	0.1878	0.0232	0.0169	0.169	-0.0351	0.2696	101.8056	83.8652	-2.3641
13	6.656	3.1445	-2.0662	2.3882	-1.1117	8.0873	-0.2518	1.0292	-0.6188	-0.2938	0.453	0.1958	-0.0253	-0.1837	0.025	0.5156	-0.1084	-0.0544	0.39	-0.0999	0.5035	94.7175	78.216	-18.8097
14	5.6201	4.6009	-1.5712	7.2052	-1.7259	2.3042	-0.1644	-0.0647	-0.2726	0.2472	-0.0367	-0.0232	0.2617	-0.1448	0.1707	0.2451	0.0217	-0.0043	0.2317	0.009	0.2696	91.3364	90.5733	-13.5638
15	2.7434	-2.3287	-0.2954	3.5051	-2.4835	5.9805	0.1687	0.9314	0.6955	-0.4525	-0.3624	-0.7406	-0.424	0.8348	0.0953	0.333	-0.121	0.0088	0.4104	0.0538	0.3514	106.8683	95.4217	-14.2729
16	1.263	1.7679	-0.3755	8.8837	1.068	1.3546	-0.015	0.0212	-0.2315	-0.1584	-0.0347	-0.5579	0.0143	0.1009	0.064	0.2289	-0.0006	0.0122	0.2584	0.0126	0.2225	105.6682	79.8181	-3.6626
17	1.2889	0.0323	-0.4196	1.8583	-3.2579	6.6879	-0.0584	-0.0475	0.1657	0.1092	0.0567	0.0226	-0.4868	-0.1987	-0.0448	0.1988	-0.0073	-0.0127	0.1191	-0.0103	0.197	98.0814	93.6913	5.7505
18	6.0159	1.8204	2.0442	6.773	-1.33	3.4653	0.4086	-1.0754	0.1477	1.2504	-0.359	0.9297	-0.0343	-1.4909	0.0958	0.4962	-0.0339	0.1394	0.4815	-0.086	0.4047	88.1108	91.1023	22.1529
19	7.1182	3.0701	-1.8996	5.5143	0.0454	3.9783	0.0736	-0.1027	0.0945	0.3542	-0.0623	-0.2185	-0.0757	0.3849	-0.0001	0.2385	0.0066	-0.0224	0.2246	0.0198	0.1707	102.6148	85.8729	18.1945
20	7.0043	2.1521	4.7436	4.9226	3.0826	6.4421	-0.0867	-0.9301	-0.4771	1.5804	0.6104	-0.1018	-1.0259	-0.9342	-0.4276	0.5812	-0.0368	0.0115	0.4544	0.1812	0.3635	142.5423	118.6764	29.2248

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 9 through 31 )	B	9 - 31
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 32 through 63 )	B	32 - 63
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 64 through 78 )	B	64 - 78
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 79 through 91 )	B	79 - 91
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 92 through 106 )	B	92 - 106
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 5 through 31 )	C	5 - 31
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 32 through 63 )	C	32 - 63
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 64 through 78 )	C	64 - 78
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 79 through 105 )	C	79 - 105
10	X-RAY DIFFRACTION	10	chain 'R' and (resid 4 through 8 )	R	4 - 8
11	X-RAY DIFFRACTION	11	chain 'R' and (resid 9 through 32 )	R	9 - 32
12	X-RAY DIFFRACTION	12	chain 'R' and (resid 33 through 63 )	R	33 - 63
13	X-RAY DIFFRACTION	13	chain 'R' and (resid 64 through 78 )	R	64 - 78
14	X-RAY DIFFRACTION	14	chain 'R' and (resid 79 through 91 )	R	79 - 91
15	X-RAY DIFFRACTION	15	chain 'R' and (resid 92 through 105 )	R	92 - 105
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 5 through 31 )	A	5 - 31
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 32 through 63 )	A	32 - 63
18	X-RAY DIFFRACTION	18	chain 'A' and (resid 64 through 78 )	A	64 - 78
19	X-RAY DIFFRACTION	19	chain 'A' and (resid 79 through 106 )	A	79 - 106
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 4 through 8 )	B	4 - 8

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