PDB-6vu7: Crystal structure of YbjN, a putative transcription regulator fro...

ID or keywords:

Entry

Database: PDB / ID: 6vu7

Title

Crystal structure of YbjN, a putative transcription regulator from E. coli

Components

YbjN protein

Keywords

TRANSCRIPTION / STRUCTURAL GENOMICS / CSGID / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / NIAID / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES

Function / homology

Putative sensory transduction regulator YbjN / Putative bacterial sensory transduction regulator / YbjN protein

Function and homology information

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.59 Å

Authors

Stogios, P.J. / Evdokimova, E. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal structure of YbjN, a putative transcription regulator from E. coli
Authors: Stogios, P.J.

History

Deposition	Feb 14, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 11, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 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	6vu7.cif.gz	259.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6vu7.ent.gz	186.1 KB	Display	PDB format
PDBx/mmJSON format	6vu7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6vu7_validation.pdf.gz	249.7 KB	Display	wwPDB validaton report
Full document	6vu7_full_validation.pdf.gz	249.6 KB	Display
Data in XML	6vu7_validation.xml.gz	1 KB	Display
Data in CIF	6vu7_validation.cif.gz	5.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vu/6vu7 ftp://data.pdbj.org/pub/pdb/validation_reports/vu/6vu7	HTTPS FTP

-
Related structure data

Related structure data	5fr7S S: Starting model for refinement
Similar structure data	5zg2-d 3hxj-2 4ino-d 4rgz-2 4elu-d 3pvz-2 3n2q-1 5e3c-d 5cbr-1 6hq3-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: CSGID-IDP96265

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: YbjN protein

B: YbjN protein

C: YbjN protein

D: YbjN protein

hetero molecules

70.8 kDa, 4 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)	54.462, 110.891, 59.924
Angle α, β, γ (deg.)	90.000, 116.708, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	YbjN protein Mass: 17676.000 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: ybjN, EC55989_0898 / Plasmid: pMCSG68SBPTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Gold / References: UniProt: B7LD46
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.29 Å³/Da / Density % sol: 46.2 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.2 Details: 0.1 M diammionium citrate, 0.1 M MES pH 5.2, 26% (w/v) PEG3350, 2% isopropanol

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 9, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.59→30 Å / Num. obs: 19643 / % possible obs: 99.7 % / Redundancy: 3.2 % / B_iso Wilson estimate: 38.08 Å² / R_merge(I) obs: 0.126 / R_pim(I) all: 0.083 / Net I/σ(I): 13.59
Reflection shell	Resolution: 2.6→2.64 Å / R_merge(I) obs: 0.597 / Mean I/σ(I) obs: 2.68 / Num. unique obs: 961 / CC_1/2: 0.536 / R_pim(I) all: 0.536

-
Processing

Software

Name	Version	Classification
PHENIX	1.15_3448	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5fr7

5fr7

Resolution: 2.59→29.93 Å / SU ML: 0.4054 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.9029
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2946	984	5.01 %	RANDOM
R_work	0.2375	18639	-	-
obs	0.2403	19623	99.3 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 48.61 Å²

Refinement step

Cycle: LAST / Resolution: 2.59→29.93 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4364	0	2	32	4398

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0029	4445
X-RAY DIFFRACTION	f_angle_d	0.596	6051
X-RAY DIFFRACTION	f_chiral_restr	0.0426	723
X-RAY DIFFRACTION	f_plane_restr	0.0034	782
X-RAY DIFFRACTION	f_dihedral_angle_d	21.0767	1605

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 (%)
2.59-2.73	0.3851	137	0.3258	2591	X-RAY DIFFRACTION	96.88
2.73-2.9	0.3498	141	0.314	2634	X-RAY DIFFRACTION	99.78
2.9-3.12	0.3407	137	0.2958	2671	X-RAY DIFFRACTION	99.93
3.12-3.44	0.3394	142	0.2697	2676	X-RAY DIFFRACTION	99.96
3.44-3.93	0.2984	143	0.2259	2685	X-RAY DIFFRACTION	99.93
3.93-4.95	0.2614	142	0.1915	2693	X-RAY DIFFRACTION	99.65
4.95-29.93	0.2335	142	0.1988	2689	X-RAY DIFFRACTION	98.95

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	3.24986490819	2.30509771638	-3.33600140362	2.55956934245	-0.76683463314	6.32165847544	0.415502751965	-0.896950871315	0.272342644606	0.0990166290273	-0.407266850219	-0.118150987832	-0.486440650691	0.23934876649	0.128774019971	0.370932933062	-0.013090539259	-0.00236921910901	0.366274488584	0.00143272450525	0.344638456678	24.221990667	-6.67570019805	11.4770474291
2	8.55879303738	1.15598783115	-1.92225020489	6.39136610913	3.76635611637	3.11739749505	0.000585250480198	-0.16224416615	-0.420457542948	-0.0112145663981	-0.158522284373	0.297760300509	0.0895329193435	-0.0928138301349	0.289047103057	0.289990102139	-0.0241770628342	-0.00165549183549	0.382639742153	0.0395056497866	0.196358355639	11.844993564	-11.8960217194	15.030114027
3	6.58104244921	1.88280105365	2.30373115541	0.712462310869	-0.0177225849071	3.28049278329	0.235909283847	-0.0583204009983	0.213825223711	0.132311578542	-0.103536227587	0.00664002147172	0.169050564151	-0.360591435147	-0.159850205914	0.351078901282	0.0491065121101	0.00682444543183	0.274787551715	-0.0454681494676	0.285691877175	3.30057913782	-12.6728535533	1.17527980006
4	9.12596078065	4.68391892195	0.297233663264	2.85307323375	0.236011619304	1.27232238189	0.175278970127	0.0803255128237	0.0466797232441	0.0379381148849	-0.120804707078	0.0670416139047	-0.0236145119963	-0.151235251653	-0.0753248528668	0.32039755897	0.0484044079377	-0.0382106749658	0.313569120844	-0.0140896820529	0.24919267889	6.58965607475	-8.55494866073	1.89171765836
5	7.01826925398	3.27649989285	0.44760344173	5.7806129862	4.2492178552	7.81405109802	-0.373823459108	1.12206816676	0.537425294587	-0.55307277205	0.215124825488	0.381764950735	-0.67419596366	-0.195454679845	0.104616310039	0.400852555358	0.0406001320174	-0.0197009861767	0.368677193035	0.15325531866	0.427777862115	20.7250174426	0.707888709271	-19.4069807165
6	3.76901355658	1.95348522846	2.49172647357	1.82892260506	0.821061401221	2.90360857402	0.0205519107749	0.057485004452	-0.0363683902406	-0.135563296484	-0.00599066890512	0.0322026121314	0.0409959921507	0.0404490158116	0.00887352273328	0.295113073453	0.0520461130681	0.0682054161035	0.28294424164	-0.0180756071591	0.26332682695	11.5325086998	-10.4082513726	-15.1153711482
7	3.01617876148	-2.57985504769	4.4172505098	6.63186018047	-2.37218288093	6.92209338402	-0.274373782262	0.693136721079	-0.672215439826	-0.873881638727	0.674793900577	0.47577979316	0.372826239014	-0.226361342745	-0.302359562825	0.413303730156	-0.130768673046	-0.0240019719584	0.475436720919	-0.0742520624712	0.445915784337	18.7050302403	-32.7150316209	-36.664630335
8	6.29118380663	-3.02012872438	-5.88517817353	2.5922558903	2.9227266944	5.51746379209	-0.973029611735	-0.355713085371	1.69744691001	-0.125965271496	1.66394861321	-1.04572821489	1.89096156381	0.216839144929	-0.81971215456	0.555709556703	-0.0753612918405	-0.0727565277321	0.365470893457	0.0680547219563	0.663865414757	25.7751288406	-22.797500645	-41.3635222746
9	7.81779165893	2.15570480169	2.17406899779	1.50380996195	-1.25029975169	4.78930052236	-0.211931041067	0.284905932849	0.24079322267	-0.258026708224	0.117977770464	-0.105316931836	-0.184237369053	-0.15488180284	0.0916385795972	0.300496635896	0.00922542000663	0.0109997647176	0.313256249307	-0.0675868922051	0.212893907547	30.9147454526	-20.8731082296	-31.6101728583
10	4.33638597333	3.5800070559	1.40825455634	4.26726682677	0.0545239197408	1.36315440994	0.0260870863371	-0.0966393606441	-0.0653963710994	-0.00608705869142	-0.00143709564341	0.0293462927403	0.0194374166592	-0.0976687664402	-0.0169073229967	0.22032012862	0.0956106378402	-0.0360942232755	0.222837253738	-0.0367191902643	0.272031025847	36.5488536012	-22.5772851803	-22.0030780105
11	7.35520422228	6.21300821737	-0.146999425317	8.58177333109	1.55624246611	2.1342027862	-0.0126204395589	-0.340988574555	0.809597215963	-0.277869450832	-0.0939142128772	0.922980726688	-0.388258008307	-0.320535933356	0.11817924569	0.377493745368	0.104067494384	-0.026803525925	0.43139702332	0.0239081378574	0.429695720762	23.1214624742	-21.0287786309	-23.5358190186
12	4.26111109314	3.62786716611	-4.33634321359	3.35112361389	-3.43776449718	6.17991580667	0.0836782794573	0.395428500955	0.733143589786	0.729567438358	1.04208621818	0.237932993889	-0.846871506441	-0.248492643593	-0.890879925201	0.473004736367	0.11313691884	-0.0519363105685	0.360627489117	-0.14081963052	0.584187252973	36.652645762	-6.14188560469	-25.3652206877
13	3.67000494987	-4.93626471611	-0.272995728055	9.45624323292	-3.94938349917	8.12021756224	-0.0989101140203	-0.95076368886	-0.523591616741	0.22907811026	0.500217921556	1.51007957867	-0.116091072463	-0.645062719797	-0.409844689802	0.305350473028	0.00305354715936	0.0067783101368	0.481827185729	-0.00663096224983	0.556345174046	16.1860262746	-43.102250051	-11.6786319977
14	7.75645873823	-3.30276034991	1.35551806848	7.7815163588	-5.76836109014	4.49184862726	-0.506936165776	-0.638287077808	-0.0854333129849	0.412492830147	-0.427897925584	0.0127550549815	-0.218475993266	-0.0655899420087	0.956186506664	0.452262812929	-0.0643161515825	-0.0764601029717	0.437102584992	-0.0397626121463	0.544954975083	24.4051851959	-44.3785525758	-3.49044821071
15	6.50993196861	5.22859729417	-0.934873324849	4.83544106435	0.964066749796	4.77808401392	0.701519872726	-1.00767661222	0.100353229712	0.770876090679	-0.656321800576	0.193552627697	0.573602609605	0.384612985947	-0.0369920463182	0.431282328503	0.0570468742399	-0.0324648864103	0.321279318737	0.0662421476172	0.363178902241	31.9447776073	-39.6313849251	-6.12192835759
16	7.3994303344	0.900908333684	1.0998117068	1.52444721094	-0.661610435959	1.89855409771	0.225028359546	-0.563587068324	-0.103815810741	0.195802914226	-0.16338428323	0.0859565056291	0.141785933622	-0.13984566895	-0.0496966622284	0.336788925521	0.0299952669466	-0.0071432701583	0.189267971558	-0.00767402595292	0.270965532359	35.9516526942	-30.1298873661	-11.4536576043
17	9.15379811434	2.48689433028	2.88425709357	4.26481578178	2.33612550364	2.58516494802	0.341051429082	0.141938972247	-1.32663748776	-0.355909711405	-0.0946514198993	-0.580914123096	0.306068415962	0.109812401129	-0.275275018111	0.444955838428	0.00368393540981	-0.0218024422131	0.21134566498	0.0555330644874	0.488009177378	36.5878519373	-40.3298525328	-15.7361880742

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 18 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 19 through 39 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 40 through 81 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 82 through 143 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 2 through 51 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 52 through 143 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 2 through 18 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 19 through 28 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 29 through 64 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 65 through 112 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 113 through 136 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 137 through 145 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 3 through 18 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 19 through 30 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 31 through 51 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 52 through 112 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 113 through 142 )

-
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

-
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

-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

-
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