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

ID or keywords:

Entry

Database: PDB / ID: 6fal

Title

Tryptophan Repressor TrpR from E.coli with 3-Indolepropionic 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 / 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: 1.2 Å

Authors

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

Funding support

Germany, 1items

Citation

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

History

Deposition	Dec 15, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 30, 2019	Provider: repository / Type: Initial release
Revision 1.1	Dec 25, 2019	Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6fal.cif.gz	133.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6fal.ent.gz	110.9 KB	Display	PDB format
PDBx/mmJSON format	6fal.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fa/6fal ftp://data.pdbj.org/pub/pdb/validation_reports/fa/6fal	HTTPS FTP

-
Related structure data

Related structure data	6f9kC C: citing same article (ref.)
Similar structure data	1jhg-1 5udm-2 2jlh-1 5udn-2 1r5x-d 1rlm-3 4rs6-1 1rlm-2 6wzr-2 6r8a-4 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#168 - Dec 2013 DNA Helicase similarity (1)

Deposited unit

A: Trp operon repressor

B: Trp operon repressor

hetero molecules

27.2 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)	36.070, 45.250, 60.670
Angle α, β, γ (deg.)	90.000, 104.020, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Trp operon repressor Mass: 13386.184 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: chain A of a dimer / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trpR, rtrY, b4393, JW4356 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0A881
#2: Chemical	ChemComp-IOP / INDOLYLPROPIONIC ACID / 3-Indolepropionic acid Mass: 189.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₁H₁₁NO₂
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.13 Å³/Da / Density % sol: 42.37 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2M MgCl2 0.1M Tris HCl, pH8.5 30% PEG 4000

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X10SA / Wavelength: 0.97796 Å

Detector

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

Radiation

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

Radiation wavelength

Wavelength: 0.97796 Å / Relative weight: 1

Reflection

Resolution: 1.2→35.875 Å / Num. obs: 59052 / % possible obs: 98.9 % / Redundancy: 6.157 % / B_iso Wilson estimate: 11.37 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.059 / R_rim(I) all: 0.064 / Χ²: 0.969 / Net I/σ(I): 19.03 / Num. measured all: 363608

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.2-1.23	5.11	0.253	6.02	20048	4384	3923	0.951	0.283	89.5
1.23-1.26	5.738	0.214	7.63	24347	4263	4243	0.969	0.236	99.5
1.26-1.3	5.762	0.183	8.68	23960	4173	4158	0.979	0.202	99.6
1.3-1.34	5.645	0.158	9.6	22742	4064	4029	0.982	0.175	99.1
1.34-1.38	6.018	0.142	10.89	23460	3922	3898	0.987	0.156	99.4
1.38-1.43	6.197	0.119	13.07	23437	3783	3782	0.991	0.13	100
1.43-1.49	6.259	0.103	15.06	22934	3674	3664	0.992	0.112	99.7
1.49-1.55	6.125	0.084	18.03	21476	3518	3506	0.995	0.092	99.7
1.55-1.62	6.301	0.076	20.16	21277	3400	3377	0.995	0.083	99.3
1.62-1.69	6.683	0.07	22.47	21525	3220	3221	0.996	0.076	100
1.69-1.79	6.662	0.063	24.84	20499	3082	3077	0.997	0.068	99.8
1.79-1.89	6.507	0.059	26.2	19176	2950	2947	0.997	0.064	99.9
1.89-2.03	6.235	0.053	27.91	16966	2737	2721	0.997	0.058	99.4
2.03-2.19	6.877	0.052	31.74	17508	2544	2546	0.998	0.056	100
2.19-2.4	6.713	0.05	32.7	15956	2380	2377	0.997	0.054	99.9
2.4-2.68	6.4	0.049	32.67	13535	2117	2115	0.997	0.053	99.9
2.68-3.09	6.311	0.049	32.99	11941	1896	1892	0.997	0.053	99.8
3.09-3.79	6.692	0.056	35.13	10774	1610	1610	0.996	0.061	100
3.79-5.36	6.076	0.06	33.62	7619	1259	1254	0.993	0.066	99.6
5.36-35.875	6.219	0.062	33.8	4428	714	712	0.993	0.068	99.7

-
Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	1.2 Å	35.87 Å
Translation	1.2 Å	35.87 Å

-
Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.2→35.875 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 15.93

	R_factor	Num. reflection	% reflection
R_free	0.179	2953	5 %
R_work	0.1618	-	-
obs	0.1627	59043	98.97 %

Solvent computation

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

Displacement parameters

B_iso max: 107.07 Å² / B_iso mean: 22.3345 Å² / B_iso min: 6.05 Å²

Refinement step

Cycle: final / Resolution: 1.2→35.875 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1586	0	46	225	1857
B_iso mean	-	-	14.92	28.8	-
Num. residues	-	-	-	-	194

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	1674
X-RAY DIFFRACTION	f_angle_d	1.123	2265
X-RAY DIFFRACTION	f_chiral_restr	0.074	252
X-RAY DIFFRACTION	f_plane_restr	0.008	294
X-RAY DIFFRACTION	f_dihedral_angle_d	12.431	661

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 21

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.1981-1.2177	0.2525	118	0.2211	2238	2356	84
1.2177-1.2387	0.199	141	0.1957	2677	2818	100
1.2387-1.2612	0.1889	141	0.1861	2677	2818	100
1.2612-1.2855	0.1876	142	0.1751	2710	2852	100
1.2855-1.3117	0.182	138	0.1787	2618	2756	99
1.3117-1.3403	0.1939	141	0.1726	2678	2819	99
1.3403-1.3714	0.1964	141	0.1734	2675	2816	99
1.3714-1.4057	0.1698	141	0.1621	2671	2812	100
1.4057-1.4438	0.1652	142	0.165	2697	2839	100
1.4438-1.4862	0.153	141	0.1587	2676	2817	100
1.4862-1.5342	0.1596	139	0.1472	2660	2799	100
1.5342-1.589	0.154	142	0.1461	2680	2822	99
1.589-1.6527	0.1775	143	0.151	2720	2863	100
1.6527-1.7279	0.166	141	0.1514	2684	2825	100
1.7279-1.819	0.1862	141	0.153	2679	2820	100
1.819-1.9329	0.1785	143	0.1517	2708	2851	100
1.9329-2.0822	0.1332	141	0.1462	2689	2830	100
2.0822-2.2917	0.1469	143	0.1375	2723	2866	100
2.2917-2.6232	0.1618	143	0.1523	2713	2856	100
2.6232-3.3046	0.2032	144	0.1685	2737	2881	100
3.3046-35.8908	0.212	147	0.1797	2780	2927	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	2.6843	0.2467	-0.1158	2.8674	0.3648	2.4674	0.0055	0.0009	0.2938	0.0323	-0.0243	-0.1613	-0.3304	0.1423	-0.0468	0.0645	-0.0116	-0.0065	0.0652	0.0151	0.0841	-6.4191	12.8299	-22.8335
2	0.8403	-0.18	0.4231	0.8459	-0.1473	3.1347	-0.0619	-0.0787	-0.0847	0.1807	0.0038	0.0185	0.218	-0.0634	0.0769	0.1135	0.0072	0.0124	0.057	0.0105	0.068	-5.8305	-1.8153	-12.7319
3	5.8455	-3.492	-5.1472	7.2448	0.4833	6.4002	0.0517	-0.5607	0.3886	0.592	0.1746	0.0726	-0.8097	0.0318	-0.1146	0.439	0.0079	-0.0606	0.2695	0.0257	0.214	-1.089	-3.7301	5.479
4	4.8458	-0.8934	-0.9584	2.3334	1.2313	0.7109	-0.1672	-0.2005	-0.0802	0.5952	0.067	-0.2358	-0.1723	0.0477	-0.2527	0.3077	0.0347	-0.0421	0.136	-0.0225	0.0742	-1.8882	8.5297	-0.6993
5	3.9806	-0.0145	0.0538	2.0052	1.4221	3.0542	0.1322	-0.6902	0.166	0.5539	-0.0549	0.3584	-0.0606	-0.4558	0.1601	0.2998	0.0594	0.1844	0.271	0.0429	0.0823	-17.3931	5.9291	-2.4545
6	2.8103	0.1989	-0.154	3.5289	-0.5623	2.5147	0.0375	-0.2674	-0.3819	0.2085	0.0781	0.2515	0.4749	-0.1971	-0.0295	0.1678	-0.0153	0.0043	0.112	0.0323	0.0819	-11.6695	-3.3076	-12.6634
7	1.8791	-0.0074	-1.4117	1.584	0.0483	3.4459	0.0284	-0.0178	0.0999	0.0423	0.0043	-0.1148	-0.1671	0.1012	-0.0538	0.061	-0.0092	-0.0122	0.0571	0.0055	0.0831	-2.6918	9.1095	-20.3169
8	3.5039	1.995	2.2078	7.5832	1.6776	2.1849	-0.1755	0.4596	-0.0251	-0.7635	0.2641	-0.0381	0.5741	0.0128	-0.0393	0.3	-0.04	0.0166	0.2538	0.0286	0.2474	10.5097	10.1931	-34.941
9	2.1961	1.1308	0.6797	3.1793	0.3144	1.8719	-0.132	0.2518	-0.1098	-0.169	0.0989	-0.2631	-0.0343	0.3143	-0.0035	0.0623	0.0082	0.0282	0.134	-0.0294	0.1676	6.7105	-1.2231	-28.8876
10	1.5363	0.0087	-0.5716	3.6982	-2.0929	2.6186	-0.046	0.4083	0.2863	-0.1895	-0.001	0.0047	-0.4887	-0.0413	0.014	0.2084	-0.0248	-0.017	0.1411	0.0096	0.1373	-7.7485	3.0192	-35.9962

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 (resid 10 through 31 )	A	10 - 31
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 32 through 63 )	A	32 - 63
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 64 through 78 )	A	64 - 78
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 79 through 93 )	A	79 - 93
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 94 through 106 )	A	94 - 106
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 13 through 32 )	B	13 - 32
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 33 through 63 )	B	33 - 63
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 64 through 78 )	B	64 - 78
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 79 through 90 )	B	79 - 90
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 91 through 109 )	B	91 - 109

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
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

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-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

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
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

-
Yorodumi