PDB-6ejz: Tryptophan Repressor TrpR from E.coli variant S88Y with Indole-3-...

ID or keywords:

Entry

Database: PDB / ID: 6ejz

Title

Tryptophan Repressor TrpR from E.coli variant S88Y with Indole-3-acetic acid as ligand

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 / cytoplasm
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.9 Å

Authors

Stiel, A.C. / Shanmugaratnam, S. / Herud-Sikimic, O. / Juergens, G. / Hocker, B.

Funding support

Germany, 1items

Citation

Journal: Nature / Year: 2021
Title: A biosensor for the direct visualization of auxin
Authors: Herud-Sikimic, O. / Stiel, A.C. / Kolb, M. / Shanmugaratnam, S. / Berendzen, K.W. / Feldhaus, C. / Hocker, B. / Juergens, G.

History

Deposition	Sep 24, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 6, 2019	Provider: repository / Type: Initial release
Revision 1.1	Apr 7, 2021	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2	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
Revision 1.3	Oct 1, 2025	Group: Advisory / Derived calculations / Structure summary Category: pdbx_entry_details / pdbx_validate_close_contact / struct_conn

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6ejz.cif.gz	188.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6ejz.ent.gz	152.2 KB	Display	PDB format
PDBx/mmJSON format	6ejz.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6ejz_validation.pdf.gz	484.9 KB	Display	wwPDB validaton report
Full document	6ejz_full_validation.pdf.gz	486.3 KB	Display
Data in XML	6ejz_validation.xml.gz	22.5 KB	Display
Data in CIF	6ejz_validation.cif.gz	30 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ej/6ejz ftp://data.pdbj.org/pub/pdb/validation_reports/ej/6ejz	HTTPS FTP

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Related structure data

Related structure data	6ejwC 6ekpC 6elbC 6elfC 6elgC 6eniC 6ennC 1troS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6ejw-1 1zt9-1 6ejw-2 6f7f-2 4p2k-d 5amt-2 1e3r-d 1snx-2 1j5p-d 6f7f-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	#110 - Feb 2009 Auxin and TIR1 Ubiquitin Ligase similarity (1) #168 - Dec 2013 DNA Helicase similarity (1)

Deposited unit

A: Trp operon repressor

B: Trp operon repressor

C: Trp operon repressor

D: Trp operon repressor

hetero molecules

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

1

A: Trp operon repressor

C: Trp operon repressor

hetero molecules

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

2

B: Trp operon repressor

D: Trp operon repressor

hetero molecules

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

Unit cell

Length a, b, c (Å)	82.440, 82.440, 75.650
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: 13517.380 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain 55989 / EAEC) (bacteria) Strain: 55989 / EAEC / Gene: trpR, EC55989_5055 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: B7LEN9
#2: Chemical	ChemComp-IAC / 1H-INDOL-3-YLACETIC ACID / INDOLE ACETIC ACID Mass: 175.184 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₁₀H₉NO₂
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.7 Å³/Da / Density % sol: 54.4 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: 0.1 M citric acid pH 3.5 2M ammonium sulfate

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X10SA / Wavelength: 1.00001 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2015

Radiation

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

Radiation wavelength

Wavelength: 1.00001 Å / Relative weight: 1

Reflection

Resolution: 1.9→46.175 Å / Num. obs: 40110 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 12.819 % / B_iso Wilson estimate: 35.3 Å² / CC_1/2: 1 / R_merge(I) obs: 0.08 / R_rim(I) all: 0.084 / Χ²: 1.009 / Net I/σ(I): 19.83

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
1.9-1.95	12.42	1.924	1.45	2896	0.613	2.006	98.2
1.95-2	13.166	1.462	2.08	2891	0.772	1.521	100
2-2.06	12.969	1.187	2.62	2794	0.822	1.236	100
2.06-2.12	12.697	0.783	4	2747	0.924	0.816	100
2.12-2.19	12.09	0.589	5.28	2621	0.95	0.615	100
2.19-2.27	12.469	0.473	6.55	2563	0.97	0.493	100
2.27-2.35	13.367	0.356	8.79	2466	0.984	0.37	100
2.35-2.45	13.306	0.286	10.57	2372	0.99	0.297	100
2.45-2.56	13.199	0.216	13.33	2276	0.994	0.224	100
2.56-2.68	13.065	0.151	17.95	2169	0.997	0.157	100
2.68-2.83	12.223	0.129	20.02	2086	0.997	0.135	100
2.83-3	12.898	0.1	25.36	1940	0.999	0.104	100
3-3.21	13.555	0.071	33.78	1857	0.999	0.073	100
3.21-3.46	13.319	0.05	44.06	1726	1	0.052	100
3.46-3.79	12.824	0.044	51.57	1592	0.999	0.045	100
3.79-4.24	11.726	0.037	54.7	1444	1	0.038	100
4.24-4.9	12.98	0.031	61.47	1271	1	0.033	100
4.9-6	13.001	0.033	59.13	1077	1	0.035	100
6-8.48	11.721	0.031	61.37	849	1	0.032	100
8.48-46.175	12.672	0.023	74.91	473	1	0.024	99.4

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	5.71 Å	46.18 Å
Translation	5.71 Å	46.18 Å

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX		refinement
PDB_EXTRACT	3.22	data extraction
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1tro

1tro

Resolution: 1.9→46.175 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.5

	R_factor	Num. reflection	% reflection
R_free	0.2177	2006	5 %
R_work	0.1841	-	-
obs	0.1857	40086	99.8 %

Solvent computation

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

Displacement parameters

B_iso max: 123.8 Å² / B_iso mean: 44.2237 Å² / B_iso min: 23.73 Å²

Refinement step

Cycle: final / Resolution: 1.9→46.175 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3308	0	118	220	3646
B_iso mean	-	-	49.4	46.76	-
Num. residues	-	-	-	-	408

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	3504
X-RAY DIFFRACTION	f_angle_d	0.693	4719
X-RAY DIFFRACTION	f_chiral_restr	0.038	516
X-RAY DIFFRACTION	f_plane_restr	0.004	611
X-RAY DIFFRACTION	f_dihedral_angle_d	7.547	2756

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.8972-1.9446	0.348	140	0.3145	2651	2791	98
1.9446-1.9972	0.3073	143	0.2732	2719	2862	100
1.9972-2.0559	0.3094	143	0.2445	2713	2856	100
2.0559-2.1223	0.2454	143	0.2105	2717	2860	100
2.1223-2.1982	0.2599	142	0.1911	2703	2845	100
2.1982-2.2862	0.2323	144	0.1915	2738	2882	100
2.2862-2.3902	0.2313	142	0.189	2692	2834	100
2.3902-2.5162	0.2384	142	0.1866	2711	2853	100
2.5162-2.6739	0.228	144	0.1825	2728	2872	100
2.6739-2.8803	0.2726	144	0.1925	2728	2872	100
2.8803-3.1701	0.214	143	0.1793	2729	2872	100
3.1701-3.6286	0.2029	144	0.1636	2729	2873	100
3.6286-4.571	0.1696	144	0.1538	2734	2878	100
4.571-46.1888	0.1996	148	0.1918	2788	2936	99

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	6.4648	1.9411	-0.5816	3.3787	0.6392	0.2897	-0.0757	0.6285	0.2624	-0.7621	-0.0531	-0.4074	0.066	0.4356	-0.3647	0.3734	0.1248	0.1864	0.5565	0.1499	0.3512	27.7796	-2.6528	-8.517
2	5.1988	-1.7851	2.9647	5.4433	1.506	3.0105	-0.6273	0.9996	0.9355	-1.5179	1.1413	-0.1141	1.3147	-0.4304	-0.4407	0.7182	-0.1938	-0.0511	0.9479	0.1399	0.4647	39.7907	-20.6695	4.1344
3	2.9925	3.083	-3.1379	9.2284	-3.8261	5.2942	0.3627	-0.0766	0.4975	0.0533	-0.3063	-0.0718	-0.379	0.2369	-0.0273	0.3655	0.0155	-0.032	0.2639	0.0244	0.3517	21.1505	-26.3566	4.9877
4	1.3182	-0.1315	1.2683	2.0356	0.9705	7.0136	0.0901	-0.0627	-0.1123	0.0423	0.0454	0.0662	0.4774	0.0906	-0.1865	0.2939	-0.0375	-0.0088	0.2187	0.0302	0.3294	21.2231	-41.3244	14.6768
5	4.8353	-3.2437	-2.8323	7.0381	0.7785	1.9152	-0.1737	-1.7944	-0.5453	1.0244	0.0971	0.2005	0.2918	1.5238	-0.056	0.5695	0.1189	0.0147	0.6865	0.1459	0.4272	29.8005	-45.6756	31.6663
6	9.7386	-0.1652	1.6371	3.6286	0.2147	3.2176	0.03	-0.2901	0.5179	0.2198	-0.1138	0.1296	-0.0938	0.0679	0.0779	0.2538	-0.0256	0.0464	0.2015	0.0119	0.1789	22.9224	-32.0276	26.8665
7	8.5542	6.8186	1.2519	7.8811	0.5979	2.0575	-0.0868	0.2967	-0.481	-0.4105	-0.0141	-0.206	0.4672	0.0539	0.1063	0.5505	0.0917	0.1123	0.3135	0.0304	0.3837	17.8865	-15.1352	2.1929
8	1.4813	-0.1278	-0.9583	2.8131	-0.3523	4.3695	0.0574	0.0419	0.2137	0.0808	-0.2117	-0.1727	-0.1335	0.1793	-0.0527	0.2193	-0.0053	0.0411	0.2462	0.0741	0.4016	19.9745	0.5982	11.7581
9	3.6279	-4.0831	3.8008	5.8456	-3.3395	4.6724	-0.1325	-1.9998	1.0255	1.1628	-0.1071	0.2719	-0.6802	-1.3464	0.1406	0.5901	0.0188	0.0035	0.5628	-0.1466	0.5998	11.0142	4.7523	28.5532
10	8.1195	0.1099	-1.8029	3.3433	0.6314	4.4837	-0.1329	-0.2361	-0.5291	0.2974	-0.1415	-0.113	0.2596	0.2783	0.2626	0.3923	0.0036	-0.0058	0.2816	0.0726	0.3739	18.2066	-8.9132	23.7706
11	4.5524	-2.7091	5.1168	8.9239	1.6266	8.7468	-0.3314	-1.0721	-0.3844	1.6767	0.2451	0.3896	-0.4151	0.1269	0.106	0.6426	0.0461	0.0248	0.393	0.0155	0.3275	29.7286	-58.2642	17.4261
12	4.5206	-4.8336	0.7185	8.2072	-0.5737	0.637	-0.0623	-0.037	-0.4216	0.1891	0.0653	0.8588	0.0171	-0.0698	0.021	0.3488	-0.0665	0.0055	0.309	-0.0054	0.3722	15.94	-43.3956	16.7386
13	2.8339	0.5676	-3.1493	2.8735	0.8361	9.5085	0.0077	0.0178	0.1674	-0.3121	-0.0264	-0.0088	-0.3711	0.2613	-0.0268	0.3035	-0.0039	-0.02	0.2076	0.0098	0.3346	24.2251	-31.2144	6.5848
14	3.6902	1.3143	1.6652	3.3956	1.9213	1.9908	-0.098	1.9078	0.1613	-1.0996	-0.5968	-0.7803	0.2388	1.6209	0.1298	0.7705	0.022	0.1739	0.7529	0.1652	0.4601	33.425	-31.5673	-10.1648
15	4.3562	3.6535	1.5399	4.172	-0.3913	4.2919	0.0538	-0.1106	0.3459	-0.1356	0.0007	0.0604	-0.013	0.4044	-0.0479	0.5153	0.0398	-0.0102	0.3218	-0.0152	0.3679	28.721	-42.875	-4.6685
16	3.5544	2.5017	-0.2957	4.1844	3.1742	7.5984	0.0314	0.8358	0.3133	-0.9954	0.1439	0.2669	0.1464	-0.4843	-0.2608	0.4786	-0.0571	-0.1166	0.4816	0.0562	0.4183	13.4277	-36.9257	-5.8579
17	4.7762	1.3959	-0.796	1.059	-1.5184	2.6788	0.352	-0.4572	-0.368	1.6835	0.6566	0.2667	-0.072	-0.7554	-0.8167	0.5265	0.005	0.0227	0.3301	0.1016	0.3264	11.2192	16.8378	14.4539
18	1.1703	-1.0385	-0.4085	3.0205	-0.4126	2.5199	-0.0928	-0.0812	-0.0851	0.3766	-0.1887	-0.1811	0.0327	0.2537	0.2728	0.273	-0.016	0.0095	0.3209	0.0941	0.404	24.9696	2.7354	13.9778
19	1.0747	0.4549	1.0744	2.1133	-1.8217	4.494	-0.1333	0.0571	-0.2297	-0.4224	-0.1063	0.0273	0.8051	-0.0667	-0.2298	0.3467	0.0433	0.0802	0.1718	0.0217	0.3063	17.1608	-9.5229	3.5226
20	2.5772	2.3229	-0.5672	2.1913	-0.5655	0.1525	0.3349	1.8255	-0.438	-1.027	-0.6842	-0.2215	-0.0483	-1.412	0.2706	0.701	0.0248	-0.0526	0.6696	-0.112	0.4	8.485	-9.1274	-13.1839
21	6.2696	2.3308	1.7311	7.8601	3.0986	6.0851	-0.0118	-0.3556	0.0007	0.0671	-0.2117	0.2762	0.4172	-0.4309	0.2504	0.3684	0.0266	0.0276	0.335	-0.0122	0.329	12.5657	2.0492	-7.8613

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 92 through 105 )	B	92 - 105
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 4 through 8 )	C	4 - 8
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 9 through 31 )	C	9 - 31
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 32 through 63 )	C	32 - 63
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 64 through 78 )	C	64 - 78
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 79 through 105 )	C	79 - 105
7	X-RAY DIFFRACTION	7	chain 'D' and (resid 5 through 31 )	D	5 - 31
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 32 through 63 )	D	32 - 63
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 64 through 78 )	D	64 - 78
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 79 through 105 )	D	79 - 105
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 4 through 8 )	A	4 - 8
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 9 through 32 )	A	9 - 32
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 33 through 63 )	A	33 - 63
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 64 through 78 )	A	64 - 78
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 79 through 91 )	A	79 - 91
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 92 through 106 )	A	92 - 106
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 4 through 8 )	B	4 - 8
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 9 through 32 )	B	9 - 32
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 33 through 63 )	B	33 - 63
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 64 through 78 )	B	64 - 78
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 79 through 91 )	B	79 - 91

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Movie

-
Structure viewers

+
Viewer log

-
This page

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This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi