PDB-6lxn: Crystal structure of C-terminal DNA-binding domain of Escherichia...

ID or keywords:

Entry

Database: PDB / ID: 6lxn

Title

Crystal structure of C-terminal DNA-binding domain of Escherichia coli OmpR in complex with F1-DNA

Components

(DNA (27-MER)) x 2
Transcriptional regulatory protein OmpR

Keywords

DNA BINDING PROTEIN / DNA binding protein Transcription factor / TRANSCRIPTION

Function / homology

Function and homology information

phosphorelay response regulator activity / phosphorelay signal transduction system / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / cytosol
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.93 Å

Authors

Sadotra, S. / Chen, C. / Hsu, C.H.

Funding support

Taiwan, 2items

Citation

Journal: J.Struct.Biol. / Year: 2020
Title: Structural basis for promoter DNA recognition by the response regulator OmpR.
Authors: Sadotra, S. / Lou, Y.C. / Tang, H.C. / Chiu, Y.C. / Hsu, C.H. / Chen, C.

History

Deposition	Feb 11, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 23, 2020	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 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

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Download

PDBx/mmCIF format	6lxn.cif.gz	160.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6lxn.ent.gz	101.4 KB	Display	PDB format
PDBx/mmJSON format	6lxn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6lxn_validation.pdf.gz	461.9 KB	Display	wwPDB validaton report
Full document	6lxn_full_validation.pdf.gz	466.5 KB	Display
Data in XML	6lxn_validation.xml.gz	11.5 KB	Display
Data in CIF	6lxn_validation.cif.gz	14.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lx/6lxn ftp://data.pdbj.org/pub/pdb/validation_reports/lx/6lxn	HTTPS FTP

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Related structure data

Related structure data	6lxlSC 6lxmC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4l4y-d 4zyn-2 6uqq-2 4l9b-d 4lgr-d 5w0t-d 4k95-8 4bq7-2 4nzy-d 4bq7-1 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	#67 - Jul 2005 TATA-Binding Protein similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #253 - Jan 2021 Expressome similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #84 - Dec 2006 Transposase similarity (1) #135 - Mar 2011 Integrase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #227 - Nov 2018 Telomerase similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #190 - Oct 2015 Two-component Systems similarity (11) #40 - Apr 2003 RNA Polymerase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #125 - May 2010 Parvoviruses similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #131 - Nov 2010 Inteins similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #23 - Nov 2001 DNA similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1) #97 - Jan 2008 Circadian Clock Proteins similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

C: DNA (27-MER)

D: DNA (27-MER)

A: Transcriptional regulatory protein OmpR

B: Transcriptional regulatory protein OmpR

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, two monomeric proteins in complex with double-stranded DNA

Unit cell

Length a, b, c (Å)	70.753, 70.753, 165.344
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	173
Space group name H-M	P6₃
Space group name Hall	P6c
Symmetry operation	#1: x,y,z #2: x-y,x,z+1/2 #3: y,-x+y,z+1/2 #4: -y,x-y,z #5: -x+y,-x,z #6: -x,-y,z+1/2

#1: DNA chain	DNA (27-MER) Mass: 8276.362 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#2: DNA chain	DNA (27-MER) Mass: 8308.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: Protein	Transcriptional regulatory protein OmpR Mass: 13099.091 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ompR, NCTC10764_03768 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A376JR14, UniProt: P0AA16*PLUS
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
Has ligand of interest	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: 2.8 Å³/Da / Density % sol: 60.77 %
Crystal grow	Temperature: 288 K / Method: vapor diffusion, sitting drop Details: 0.1 M Magnesium acetate tetrahydrate, 0.05 M MED monohydrate, pH 5.6, 20% v/v (+/-)-2-Methyl-2,4,pentanediol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.975 Å
Detector	Type: RAYONIX MX300-HS / Detector: CCD / Date: Mar 18, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.975 Å / Relative weight: 1
Reflection	Resolution: 2.93→28.73 Å / Num. obs: 8766 / % possible obs: 99.5 % / Redundancy: 9.4 % / B_iso Wilson estimate: 66.21 Å² / CC_1/2: 0.998 / Net I/σ(I): 45.5
Reflection shell	Resolution: 2.93→3.04 Å / Num. unique obs: 985 / CC_1/2: 0.996

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Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	refinement
HKL-2000		data scaling
PHASER		phasing
HKL-2000		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6LXL

6lxl

Resolution: 2.93→28.73 Å / SU ML: 0.3579 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.8666

	R_factor	Num. reflection	% reflection
R_free	0.2415	894	10.2 %
R_work	0.1704	-	-
obs	0.178	8766	99.5 %

Solvent computation

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

Displacement parameters

B_iso mean: 64.17 Å²

Refinement step

Cycle: LAST / Resolution: 2.93→28.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1705	1107	5	0	2817

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0095	2989
X-RAY DIFFRACTION	f_angle_d	1.1275	4266
X-RAY DIFFRACTION	f_chiral_restr	0.055	464
X-RAY DIFFRACTION	f_plane_restr	0.0075	362
X-RAY DIFFRACTION	f_dihedral_angle_d	20.4834	1603

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 (%)
2.94-3.12	0.4367	85	0.2589	772	X-RAY DIFFRACTION	51.75
3.12-3.36	0.2973	127	0.2132	1128	X-RAY DIFFRACTION	75.74
3.36-3.7	0.3025	172	0.2002	1482	X-RAY DIFFRACTION	99.64
3.7-4.23	0.2275	171	0.1682	1502	X-RAY DIFFRACTION	100
4.23-5.32	0.2142	171	0.155	1501	X-RAY DIFFRACTION	100
5.32-28.73	0.2086	168	0.1473	1487	X-RAY DIFFRACTION	97.87

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	0.203706144258	-0.212465667685	-0.1743712515	0.312054881822	0.158794821913	0.155133124239	-0.00783718142861	0.0103121361991	-0.00330027965708	-0.0105306489815	0.00424675434938	-0.0125746200373	0.0133151945484	-0.0189811233096	-0.00272995420426	2.08486594888	-0.17527517592	0.264888779783	2.20863862386	-0.00742116817545	1.82690299339	5.52860293672	-32.6344623306	-0.958814146262
2	0.127020373327	-0.061144238885	-0.00771887973206	0.0336616186516	0.00987889135265	0.0777561157994	-0.00600111674111	0.0230738431354	0.0197916830945	0.207010087213	0.0702403928512	-0.0596998603151	-0.370084614949	-0.0833113971469	-0.114791936342	0.321683705598	0.188801724392	0.139173786379	0.281848784833	0.0565861348096	0.321698001035	2.21569711368	-12.7880875726	42.8769365152
3	0.0577012804765	-0.0229106212492	0.0230243869092	0.0639731309166	-0.0146046958843	0.00826761781977	-0.026108422992	0.014135187682	0.0354000435955	0.0627689370058	0.0275638457423	0.0165468888375	-0.224809959131	-0.012202949702	0.0606375896181	0.466138442007	0.00483965811567	0.159359250758	0.253788815288	0.180408032117	0.349056215317	8.53607744222	-10.0670028979	40.4979381291
4	0.180051009992	0.118265015117	-0.0382844365936	0.13912367767	-0.0854319538566	0.0589617625653	0.0174016057936	-0.0629254471334	-0.03377879895	-0.0370611028047	-0.184616411168	0.105502946452	0.0897082030857	0.0366003534309	-0.193099794449	-0.565433432172	-0.267454413797	0.423942482576	0.0139562394659	0.116933869992	0.230026582423	1.87006250954	-24.474743154	48.2034021077
5	0.0204581827622	0.0103967812455	0.00205015031309	0.0203762980556	-0.0207588820076	0.0284596993868	0.0655086050093	0.0284744616083	-0.162722369002	-0.18324969568	-0.0514064496429	0.0516669442596	0.0777109072762	-0.0150207104815	-0.0029487437327	0.177021752136	-0.0165431265289	-0.0446337273786	0.153170626044	0.197343811847	0.170929810803	5.13434692818	-33.1598263475	46.8406909097
6	0.223730979184	0.136021619846	0.0570533314469	0.13546884151	0.0906901301918	0.529547536415	0.0237910532612	0.00332751438744	-0.161698572339	-0.0615465882954	0.0551641084394	0.133660639146	-0.071736657401	0.120771700541	-0.0762675279544	0.491763511928	0.185161718448	-0.0240992493564	0.254794954922	-0.183725956439	0.428499136429	11.9582408269	-37.4956360222	47.6716644644
7	0.0829778451828	-0.0542312410518	0.0172544835092	0.0761661043981	0.00360838095966	0.00907573877803	-0.0221899276564	0.0848118535007	0.121075601387	-0.0374023044325	-0.00250980618599	-0.108477866642	-0.119896551274	0.151564765477	-0.0530247994226	0.125781204669	-0.204843353389	0.0633874591184	0.125149095237	-0.085677142381	0.416558632222	14.0558241026	-23.1565340731	48.5738476029
8	0.0486845754679	0.0832357300811	0.00989009796562	0.271367246909	-0.106424157753	0.125846127534	0.0881501399365	-0.191196199548	0.420880444325	0.280041269649	-0.00479413310595	0.16252283029	-0.254147326789	0.0557874026829	0.172986004333	0.368360776795	-0.122643473951	0.147063271066	0.241301414704	-0.104735592807	0.413156062715	8.8949696769	-20.3784822468	57.1605248379
9	0.0706968429056	-0.00216577358902	0.0608830830922	0.00179658763907	0.000773213717395	0.0846136068958	0.0184862632154	-0.159036495706	0.28372574294	0.0344650968848	0.0921617379727	0.00820006942608	-0.25911161299	-0.170950918513	0.0200544927856	0.4510005749	0.0255182444383	0.153185712628	0.440968549525	-0.0257525388884	0.524072964954	-4.12506028865	-25.276884543	62.5728832786
10	0.030767082008	-0.000185547935208	-0.0350187840348	0.0242066030007	0.00777229431786	0.0606098903202	0.115386506053	0.0118898134734	0.0319414625493	-0.0135229353933	0.0965037574316	0.00973690066849	-0.0358339049992	-0.0924101102511	0.01376849385	0.295954205383	0.156400214556	-0.1793329704	0.369869238225	0.131255620694	0.606080573053	-5.92587006696	-14.0128035085	18.3488739422
11	0.0238446181259	0.00776100941274	0.0295183762516	0.0796592273946	-0.0325345976424	0.0573529171888	0.0141088035061	0.193132429373	-0.113094954195	-0.0449777419655	-0.0763180555247	0.0141447359107	-0.142775291851	-0.153111453253	-0.0021707342771	0.888108534341	0.0620070828984	-0.280798166019	0.842173249973	0.355755496419	1.03498897808	-4.80623593404	-15.6680528033	11.4498214468
12	0.0169430184917	-0.0118955875195	-0.013079859852	0.00427318349038	0.00962985942935	0.0149030754786	0.0483578111961	0.0216856047653	0.0860039692772	0.0487037088425	0.096808734014	0.0899501487013	-0.0727982079824	-0.139335645756	-0.00832310835312	0.838214254122	0.128189979685	0.0416099934737	0.900984445426	0.306036239873	0.373724386264	-0.803598731338	-10.167398643	11.2306974613
13	0.00829198766305	-0.00485432469607	0.010401585879	0.0152085938365	-0.00582540607935	0.0173688852105	0.233428990887	0.0344359895795	-0.0847983413018	-0.0696048675639	-0.0363219841036	0.0276578311637	0.0252932996266	-0.0570906817123	-0.000862093085248	0.487197090493	-0.0359731351924	-0.0762720610475	0.483351573492	0.103557188161	0.427572814535	-0.00808836411698	-23.7171650812	15.8337391813
14	0.111146171111	-0.0324412933367	-0.00787004550626	0.00933092143916	0.00105852067946	0.00014898252101	0.0261263007573	0.000448704718217	0.02300151196	0.0166670143354	0.0156105552977	0.0902853372667	0.0332024962714	-0.0318443524269	0.160187709276	0.528287068346	-0.593397633029	-0.0684699672601	0.474810072053	0.0954831863257	0.418425843043	-2.11915858065	-27.6405876139	27.23126121
15	0.0689007758664	0.0223960335694	0.0126111091966	0.0110925702898	0.00691303441475	0.00309206655427	-0.0237473939428	0.0937297543311	-0.0463480967212	-0.291860854122	0.113935146377	-0.0959703278226	0.0955160082637	-0.0331513175439	0.0627405389303	0.791218099467	-0.114663519251	-0.192074468049	0.204851226183	0.0351225458337	0.541967087387	4.2585075712	-32.6693284277	18.3210777117
16	0.0148354277944	0.0559750827795	0.0269065570067	0.194670703128	0.0867417685001	0.0517984384192	-0.0713327434971	-0.088579556207	-0.113788596384	-0.00181605222919	0.0146703616508	0.00561881878922	0.167160703712	0.16732104592	7.81356000081E-5	0.718183418191	0.053618307064	-0.00987637152918	0.48978630245	0.0573129607532	0.454732000363	12.051437976	-35.2064803524	18.4993228869
17	0.0828630579071	-0.065293203992	0.060747726542	0.0523594452034	-0.0327771103859	0.2220016248	0.027026289441	0.0720475523919	0.150759881049	-0.147743666797	0.0894014112442	-0.00748358507089	-0.0666083282736	0.0175164523671	0.349854484561	0.230617943498	-0.0625465262908	0.111213368997	0.116899831939	0.181939446457	0.230779963463	10.0694056501	-20.3137392454	18.0036293915
18	0.0261202331749	-0.0262141442184	-0.0454536055759	0.0310969081722	0.0867117262267	0.390422028137	0.0638212298028	-0.0292325320568	0.0414897890484	0.0465721879335	0.158153770425	-0.0121112273151	-0.0137847907276	-0.08936708715	0.0330459785858	0.527004119099	0.0078567074668	0.0687404113662	0.168912402338	0.000258845121738	0.513324433441	6.32961490813	-12.6110969125	26.4988301081
19	0.0774920645741	0.198685548955	0.233055214945	0.787344515872	0.37440123822	0.917825907629	0.0398964615394	0.172328176564	0.316219365689	0.0639270800995	0.331372194767	0.374069258905	-0.176101471617	-0.175375011768	0.311020737029	0.25631254356	0.0160571565187	0.0967146708635	0.251498224705	0.0964444532488	0.37135090391	3.84586969595	-22.8676073337	28.9119502393

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 20 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 21 through 28 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 29 through 47 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 48 through 56 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 57 through 65 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 66 through 77 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 78 through 98 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 99 through 111 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 2 through 12 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 13 through 20 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 21 through 28 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 29 through 40 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 41 through 47 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 48 through 56 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 57 through 65 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 66 through 77 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 78 through 87 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 88 through 102 )

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