PDB-4yze: Crystal structure of E.coli NemR reduced form

ID or keywords:

Entry

Database: PDB / ID: 4yze

Title

Crystal structure of E.coli NemR reduced form

Components

HTH-type transcriptional repressor NemR

Keywords

TRANSCRIPTION / transcription factor / cystein-lysine sulfenamide thiol

Function / homology

Function and homology information

DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.2 Å

Authors

Li, Y. / Gray, M.J. / Jakob, U. / Xu, Z.

Citation

Journal: Antioxid.Redox Signal. / Year: 2015
Title: Does the Transcription Factor NemR Use a Regulatory Sulfenamide Bond to Sense Bleach?
Authors: Gray, M.J. / Li, Y. / Leichert, L.I. / Xu, Z. / Jakob, U.

History

Deposition	Mar 24, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 3, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Sep 27, 2023	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

-
Download

PDBx/mmCIF format	4yze.cif.gz	299.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4yze.ent.gz	245.5 KB	Display	PDB format
PDBx/mmJSON format	4yze.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4yze_validation.pdf.gz	451.3 KB	Display	wwPDB validaton report
Full document	4yze_full_validation.pdf.gz	460.3 KB	Display
Data in XML	4yze_validation.xml.gz	27.7 KB	Display
Data in CIF	4yze_validation.cif.gz	38.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yz/4yze ftp://data.pdbj.org/pub/pdb/validation_reports/yz/4yze	HTTPS FTP

-
Related structure data

Related structure data	3rd3S S: Starting model for refinement
Similar structure data	3g56-d 6ho8-1 3crj-2 4gfk-d 5f27-1 3lwj-1 7ky1-1 6srn-1 6hnx-1 6ho9-1 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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: HTH-type transcriptional repressor NemR

B: HTH-type transcriptional repressor NemR

C: HTH-type transcriptional repressor NemR

D: HTH-type transcriptional repressor NemR

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

1

A: HTH-type transcriptional repressor NemR

C: HTH-type transcriptional repressor NemR

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

2

B: HTH-type transcriptional repressor NemR

D: HTH-type transcriptional repressor NemR

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

Unit cell

Length a, b, c (Å)	67.438, 67.443, 213.864
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	HTH-type transcriptional repressor NemR Mass: 22367.189 Da / Num. of mol.: 4 / Mutation: C21S, C98S, C116S, C149S, C153S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: nemR, ydhM, b1649, JW5874 / Production host: Escherichia coli (E. coli) / References: UniProt: P67430
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.72 Å³/Da / Density % sol: 54.75 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 3.2M NaCl, 100 mM sodium acetate, pH 4.6

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 9, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 2.2→46.5 Å / Num. obs: 50363 / % possible obs: 99.9 % / Redundancy: 7.3 % / R_merge(I) obs: 0.078 / Net I/σ(I): 23.9
Reflection shell	Resolution: 2.2→2.28 Å / Redundancy: 7.5 % / R_merge(I) obs: 0.734 / Mean I/σ(I) obs: 3 / % possible all: 100

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
PHENIX	1.8.2_1309	refinement
PHASER		phasing
PDB_EXTRACT	3.15	data extraction
HKL-2000		data scaling
HKL-2000		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RD3

3rd3

Resolution: 2.2→46.5 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.56 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.255	2564	5.09 %
R_work	0.205	-	-
obs	0.207	50363	99.8 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 60.11 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→46.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5667	0	0	119	5786

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	5768
X-RAY DIFFRACTION	f_angle_d	1.031	7804
X-RAY DIFFRACTION	f_dihedral_angle_d	14.789	2027
X-RAY DIFFRACTION	f_chiral_restr	0.066	891
X-RAY DIFFRACTION	f_plane_restr	0.004	1004

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.2-2.2427	0.3312	152	0.2641	2601	X-RAY DIFFRACTION	99
2.2427-2.2885	0.3044	150	0.2465	2577	X-RAY DIFFRACTION	100
2.2885-2.3382	0.3002	146	0.2367	2653	X-RAY DIFFRACTION	100
2.3382-2.3926	0.2759	135	0.2353	2593	X-RAY DIFFRACTION	100
2.3926-2.4525	0.2987	152	0.2279	2606	X-RAY DIFFRACTION	100
2.4525-2.5188	0.2838	132	0.225	2645	X-RAY DIFFRACTION	100
2.5188-2.5929	0.2822	125	0.2355	2661	X-RAY DIFFRACTION	100
2.5929-2.6766	0.2943	140	0.2311	2617	X-RAY DIFFRACTION	100
2.6766-2.7722	0.2844	142	0.2258	2627	X-RAY DIFFRACTION	100
2.7722-2.8832	0.2687	149	0.233	2628	X-RAY DIFFRACTION	100
2.8832-3.0144	0.3198	163	0.2438	2608	X-RAY DIFFRACTION	100
3.0144-3.1733	0.3046	132	0.2373	2678	X-RAY DIFFRACTION	100
3.1733-3.372	0.2982	143	0.2222	2692	X-RAY DIFFRACTION	100
3.372-3.6323	0.2191	135	0.1987	2641	X-RAY DIFFRACTION	100
3.6323-3.9977	0.1974	132	0.175	2705	X-RAY DIFFRACTION	100
3.9977-4.5757	0.2064	160	0.1697	2675	X-RAY DIFFRACTION	100
4.5757-5.7632	0.2399	130	0.1851	2736	X-RAY DIFFRACTION	99
5.7632-46.555	0.2545	146	0.1959	2856	X-RAY DIFFRACTION	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	2.5076	1.6541	3.8221	0.8812	-0.0303	4.1115	0.1071	-0.2951	-0.1393	0.332	0.0506	-0.3558	-0.0282	0.4709	-0.0284	0.6756	0.1217	-0.2166	0.4422	0.0685	0.4965	19.2049	86.879	64.789
2	3.6561	-0.4493	1.3706	2.6944	0.336	4.0515	-0.0928	-0.076	-0.1441	-0.022	0.0009	-0.2951	0.0505	0.0505	0.142	0.5636	0.0309	-0.0742	0.2269	0.0974	0.4578	9.1408	83.9973	46.4904
3	2.5447	0.0362	-1.0901	4.8568	-1.6449	4.0915	-0.1497	0.3322	-0.0428	-0.1041	-0.0267	-0.061	0.2116	-0.0096	0.1368	0.4426	-0.0096	-0.0025	0.1867	0.0219	0.3174	1.838	77.4567	44.6789
4	0.8252	-0.1486	-0.1499	1.638	2.7808	6.3573	-0.0896	0.0239	-0.2259	-0.1566	0.188	-0.0426	0.7322	0.2818	-0.0623	0.4103	-0.0191	0.052	0.4752	-0.0687	0.3691	-3.0377	68.7212	102.6015
5	3.0509	1.3257	-1.4272	3.3706	-0.6722	2.3412	-0.0279	-0.3552	-0.1145	0.5803	-0.0273	-0.0938	-0.094	0.4306	0.0636	0.16	0.0455	-0.0086	0.611	-0.0123	0.3494	1.797	79.9201	119.0619
6	0.6692	-0.2021	-0.4388	3.5053	-1.0181	7.0359	0.0015	-0.1804	0.1211	0.3602	0.1765	0.0365	-0.4919	-0.7647	-0.1083	0.3847	0.0701	0.0614	0.399	-0.1007	0.3689	-14.8271	78.4472	72.3719
7	0.9421	-0.398	-0.2715	3.5668	-0.9812	3.4538	0.3071	0.0753	0.6511	-0.5814	-0.4499	0.2518	0.1907	-0.2348	0.0451	0.464	0.0556	-0.0226	0.3559	-0.075	0.6142	-11.761	84.094	54.2552
8	2.9914	-0.2091	-0.2843	5.0476	0.6888	8.5189	-0.0021	0.2673	-0.1738	-0.9795	-0.1133	0.7502	1.1899	-0.8427	-0.0421	0.5003	-0.1134	-0.0715	0.2928	-0.0955	0.4905	-13.5995	72.5774	47.8386
9	4.2777	2.722	0.9602	6.4683	1.1528	2.7893	-0.0495	0.3202	0.3956	-0.3055	-0.0489	0.5013	-0.0882	-0.0923	0.0966	0.4303	0.0576	-0.0592	0.1873	-0.0314	0.3653	-6.5931	85.1283	46.4312
10	4.8026	-0.4002	1.5844	5.0312	-0.4126	4.8872	0.2426	0.4844	0.0172	-1.5343	-0.1892	-0.0982	0.1158	0.4884	-0.0161	0.8422	0.1007	-0.0351	1.0986	0.1365	0.5176	4.3219	97.2032	82.6378
11	5.6455	-1.9003	-2.5564	4.4184	2.0532	2.5369	0.279	0.2504	0.6246	-0.4249	-0.1992	-0.2018	-2.0294	1.2005	0.0856	0.6944	-0.1153	-0.0969	0.6627	0.1947	0.58	6.2679	99.6122	98.7867
12	5.0305	1.2702	2.4769	1.4056	-1.4291	8.6724	-0.7445	-0.0714	1.4273	-0.2645	0.5542	0.8538	-1.564	0.8514	-0.3859	0.788	0.0522	-0.0522	0.7485	-0.2373	0.6605	-5.0138	99.8102	113.9531
13	0.0154	0.3377	0.2343	5.0937	3.5576	2.466	-0.1782	1.2828	1.615	-0.4455	-0.3835	2.6195	-2.2446	-0.5139	0.2307	0.6503	-0.2592	0.0415	1.5552	0.3778	1.6618	-11.3909	93.2822	98.3631
14	6.1886	-1.2435	1.798	4.3687	-3.4872	2.2278	-0.1681	0.1161	0.5825	0.8956	-0.2225	-0.4798	0.2228	1.5523	0.1106	0.3066	-0.4295	-0.1998	0.6573	0.1705	0.6162	7.9293	93.5325	108.6474
15	9.3564	2.386	3.5562	4.8169	-1.3321	5.546	-0.0455	0.0198	0.3931	0.4245	-0.4603	0.1205	-1.4621	-0.0273	0.189	0.0528	-0.029	-0.0067	0.6358	-0.024	0.3709	-0.119	87.9603	110.9183
16	7.0706	2.9171	4.6611	8.4667	-0.1258	4.9226	0.1992	0.071	1.1917	1.3082	-0.7816	0.8661	0.0114	-0.9185	0.6673	0.2135	0.0668	0.0336	0.7398	-0.047	0.4061	-8.5453	90.2286	117.3448

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 7:76 )	A	7 - 76
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 77:155 )	A	77 - 155
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 156:199 )	A	156 - 199
4	X-RAY DIFFRACTION	4	( CHAIN B AND RESID 8:146 )	B	8 - 146
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 147:199 )	B	147 - 199
6	X-RAY DIFFRACTION	6	( CHAIN C AND RESID 9:76 )	C	9 - 76
7	X-RAY DIFFRACTION	7	( CHAIN C AND RESID 77:119 )	C	77 - 119
8	X-RAY DIFFRACTION	8	( CHAIN C AND RESID 120:155 )	C	120 - 155
9	X-RAY DIFFRACTION	9	( CHAIN C AND RESID 156:197 )	C	156 - 197
10	X-RAY DIFFRACTION	10	( CHAIN D AND RESID 9:51 )	D	9 - 51
11	X-RAY DIFFRACTION	11	( CHAIN D AND RESID 52:75 )	D	52 - 75
12	X-RAY DIFFRACTION	12	( CHAIN D AND RESID 76:97 )	D	76 - 97
13	X-RAY DIFFRACTION	13	( CHAIN D AND RESID 98:106 )	D	98 - 106
14	X-RAY DIFFRACTION	14	( CHAIN D AND RESID 107:155 )	D	107 - 155
15	X-RAY DIFFRACTION	15	( CHAIN D AND RESID 156:177 )	D	156 - 177
16	X-RAY DIFFRACTION	16	( CHAIN D AND RESID 178:197 )	D	178 - 197

-
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://pdbjlvh1.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