PDB-8ylg: Crystal structure of Burkholderia thailandensis MftR in complex w...

ID or keywords:

Entry

Database: PDB / ID: 8ylg

Title

Crystal structure of Burkholderia thailandensis MftR in complex with operator DNA

Components

(DNA (28-MER)) x 2
MarR family transcriptional regulator

Keywords

TRANSCRIPTION / Transcription factor

Function / homology

DNA / DNA (> 10) / :

Function and homology information

Biological species

Burkholderia thailandensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Song, W.S. / Yoon, S.I.

Funding support

Korea, Republic Of, 2items

Citation

Journal: Nucleic Acids Res. / Year: 2024
Title: Structural basis of transcriptional regulation by UrtR in response to uric acid.
Authors: Song, W.S. / Ki, D.U. / Cho, H.Y. / Kwon, O.H. / Cho, H. / Yoon, S.I.

History

Deposition	Mar 6, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 13, 2024	Provider: repository / Type: Initial release
Revision 1.1	Dec 4, 2024	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8ylg.cif.gz	244.3 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	8ylg_validation.pdf.gz	440.8 KB	Display	wwPDB validaton report
Full document	8ylg_full_validation.pdf.gz	440.8 KB	Display
Data in XML	8ylg_validation.xml.gz	20 KB	Display
Data in CIF	8ylg_validation.cif.gz	28.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yl/8ylg ftp://data.pdbj.org/pub/pdb/validation_reports/yl/8ylg	HTTPS FTP

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Related structure data

Related structure data	8ylfC 8ylhC 8yliC 8yljC 8ylkC 8yllC 8ylmC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&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) #168 - Dec 2013 DNA Helicase similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #253 - Jan 2021 Expressome similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #135 - Mar 2011 Integrase similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #227 - Nov 2018 Telomerase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #84 - Dec 2006 Transposase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #23 - Nov 2001 DNA similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

A: MarR family transcriptional regulator

B: MarR family transcriptional regulator

C: DNA (28-MER)

D: DNA (28-MER)

53.9 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

Unit cell

Length a, b, c (Å)	62.554, 101.580, 109.170
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	MarR family transcriptional regulator Mass: 18337.809 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Gene: A8H32_16025 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2N8QSC4
#2: DNA chain	DNA (28-MER) Mass: 8564.541 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Burkholderia thailandensis (bacteria)
#3: DNA chain	DNA (28-MER) Mass: 8644.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Burkholderia thailandensis (bacteria)
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 300 / 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: 3.22 Å³/Da / Density % sol: 61.78 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: PEG 8000, sodium cacodylate, calcium acetate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 31, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 1.8→30 Å / Num. obs: 65149 / % possible obs: 99.6 % / Redundancy: 4.9 % / CC_1/2: 0.997 / Net I/σ(I): 23.2
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3166 / CC_1/2: 0.687 / % possible all: 99

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Processing

Software

Name	Version	Classification
PHENIX	1.15.2_3472	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: in-house Se-SAD model

Resolution: 1.8→29.89 Å / SU ML: 0.2257 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.7719
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2198	3368	5.19 %
R_work	0.1966	61544	-
obs	0.1978	64912	99.62 %

Solvent computation

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

Displacement parameters

B_iso mean: 29.18 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→29.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2445	1142	0	300	3887

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0071	3786
X-RAY DIFFRACTION	f_angle_d	0.956	5374
X-RAY DIFFRACTION	f_chiral_restr	0.0495	612
X-RAY DIFFRACTION	f_plane_restr	0.0058	511
X-RAY DIFFRACTION	f_dihedral_angle_d	19.4201	2108

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 (%)
1.8-1.83	0.3484	120	0.3123	2520	X-RAY DIFFRACTION	98.95
1.83-1.85	0.376	155	0.304	2505	X-RAY DIFFRACTION	99.14
1.85-1.88	0.3174	132	0.2852	2544	X-RAY DIFFRACTION	99.41
1.88-1.91	0.2952	145	0.2723	2506	X-RAY DIFFRACTION	99.59
1.91-1.95	0.2844	140	0.2513	2523	X-RAY DIFFRACTION	99.63
1.95-1.98	0.2856	137	0.2433	2545	X-RAY DIFFRACTION	99.74
1.98-2.02	0.2691	145	0.2426	2544	X-RAY DIFFRACTION	99.78
2.02-2.06	0.2537	134	0.2252	2538	X-RAY DIFFRACTION	99.85
2.06-2.11	0.2843	145	0.2206	2542	X-RAY DIFFRACTION	99.85
2.11-2.15	0.2447	148	0.2084	2562	X-RAY DIFFRACTION	99.93
2.15-2.21	0.2481	144	0.2047	2544	X-RAY DIFFRACTION	99.96
2.21-2.27	0.2225	146	0.197	2522	X-RAY DIFFRACTION	100
2.27-2.33	0.1846	144	0.1921	2567	X-RAY DIFFRACTION	99.96
2.33-2.41	0.2257	143	0.2002	2568	X-RAY DIFFRACTION	100
2.41-2.5	0.2473	128	0.1979	2574	X-RAY DIFFRACTION	99.96
2.5-2.6	0.2446	132	0.2005	2572	X-RAY DIFFRACTION	100
2.6-2.71	0.2438	149	0.2124	2561	X-RAY DIFFRACTION	99.96
2.71-2.86	0.2234	133	0.2146	2599	X-RAY DIFFRACTION	99.96
2.86-3.04	0.2421	122	0.2123	2593	X-RAY DIFFRACTION	99.96
3.04-3.27	0.2175	149	0.1898	2575	X-RAY DIFFRACTION	99.78
3.27-3.6	0.187	167	0.1762	2576	X-RAY DIFFRACTION	99.71
3.6-4.12	0.175	155	0.1669	2600	X-RAY DIFFRACTION	99.78
4.12-5.18	0.1776	122	0.1509	2668	X-RAY DIFFRACTION	99.29
5.18-29.89	0.1803	133	0.1781	2696	X-RAY DIFFRACTION	96.92

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	2.5553431958	0.704121185597	3.98402886079	2.25956298498	1.41147689369	8.42053415411	0.169277567072	0.538208117644	-0.226276685079	-0.164252846848	0.148675809703	-0.0454862560216	0.341059453731	-0.0255494570817	-0.296724726308	0.232330197941	0.00314036629733	0.00212333849632	0.370792292488	-0.0360961384922	0.163056783717	-7.94774993354	-34.5791463699	8.41768145331
2	5.83109289527	-7.55792697393	-5.81054809841	2.01267766767	7.34631959946	6.12693040364	0.668556620465	-0.742569925059	1.3977115006	-1.17866582353	0.812158950973	-0.754373022478	-1.48031759171	1.54285598264	-1.19005992771	0.549578349356	-0.127960770051	0.0945528484531	0.822858439266	0.0435876495888	0.413227209433	-11.5468960117	-25.3073211411	-10.2151606291
3	2.92237126655	-2.05575914901	-0.6331154855	1.40666945234	0.11804126859	0.958820523752	0.183571605397	-0.194314291163	0.206042528048	-0.000689136631719	-0.0238676516858	-0.203227603827	-0.122556879211	0.232583931521	-0.126902719465	0.227033862521	-0.0285113921581	-0.0146579514994	0.192691938672	-0.0188412664881	0.19421794723	13.2353185277	-13.4587694104	33.6072428936
4	1.48065400615	-0.230116609067	-0.390934603283	1.2505504196	0.405744087168	2.64185400127	0.0458452116954	0.361954443855	0.00240286546013	-0.0597249266742	-0.0359524842109	0.151164562742	0.0227581022018	-0.403353826111	9.38623329026E-5	0.131806948205	0.00479269430237	-0.000126127535366	0.227285801203	0.0275108255191	0.174469060415	-17.8284681997	-23.8814358458	21.0387711763
5	1.42444056655	0.697628902728	0.134288679923	1.75954428951	0.2481212386	1.26068862672	0.0782803167519	0.0958373930015	0.525646657231	0.0871006998758	-0.00451626726594	0.188204769901	-0.221966931429	-0.0871738260477	-0.100088958847	0.202182810123	0.0422148093651	0.035977420228	0.155862562511	0.0616476240131	0.224639812795	-10.0575505424	-7.73539523168	29.3159331502
6	9.28962333299	-1.31533338753	-2.73668983029	1.38641580548	0.474897872667	2.72868270635	0.235603727789	0.474565941954	0.636248327285	-0.0127799391409	0.0496347029382	0.16328015215	-0.264113835127	-0.196653388068	-0.316851863244	0.266573194358	0.0857292504737	0.016739205513	0.306167169738	0.122431733444	0.301898737808	-17.3737772587	-6.96687201557	21.9795704822
7	8.47217469716	-7.28739728954	-4.54163470397	8.48259403266	4.26297325223	5.29762918245	0.100262009319	0.300459431039	0.0135081392398	-0.0864094240226	-0.0471576370935	0.286545704609	-0.135412221212	-0.152495541017	-0.00141732179512	0.1559146426	-0.0335178634611	-0.0133678860879	0.140150881522	0.0432863541791	0.163896884163	-3.11787842414	-12.214407846	23.6570559392
8	4.76021224602	-2.65973689687	2.82077307922	6.5668871929	-4.53906236025	3.56625256899	-0.112753764624	0.522335816659	-0.467012814236	-0.345503571339	-0.0215914463796	-0.143906366538	0.152844335063	0.0760566585523	-0.0209466619402	0.191868388398	-0.0179787836204	-0.000432353648148	0.174673570557	-0.0554694856911	0.114190070165	12.8235022621	-24.1947395587	19.5779684766
9	2.81805580039	1.10177622652	-0.428780897276	2.19223362912	-0.831149234994	3.48581982466	0.0465097929175	-0.0397943888682	-0.2739306728	0.103735213577	-0.0415501446113	-0.259836096104	0.21953610646	0.297567390861	-0.00344887420219	0.167293879654	0.043833694315	-0.0388958277645	0.147408580717	-0.0311291777946	0.174586881329	16.326557156	-30.280030991	36.9186172742
10	9.39201943966	-7.28924454921	3.8301131521	5.77465387111	-4.03204460417	4.41358327223	-0.0293337696653	0.202713809185	0.121071219216	0.136687148946	-0.00347308447084	-0.314090373493	-0.212230355191	0.387429713651	0.0849650635368	0.185045443303	-0.048643366863	0.0495566142457	0.280721967776	-0.0470449706051	0.204488988384	19.3456740821	-17.7200577528	22.9610611126
11	7.55954878842	1.49681059932	-4.87114516248	7.63984537638	-3.1383542225	8.0310480868	0.133666444446	-0.449383534116	0.567856572864	0.326637695889	-0.127497483209	-0.207587709877	-0.538430270166	0.422674834326	-0.0541020731786	0.185946125008	0.00629754933521	-0.0121475566655	0.123897556038	-0.0517974744589	0.224787631258	5.72607039768	-3.39738682502	32.0459852371
12	3.80339237536	1.37047082956	3.70957395337	4.55527098919	3.905873081	7.26918357392	0.37167310226	-0.50402706847	-0.452805547667	0.0951672697011	0.172709984423	-0.302237489154	0.638749897039	1.1787528637	-0.45869269641	0.35849685107	0.0106214054739	-0.0281243678401	0.733426745163	0.046576995961	0.235193589572	-8.45260221868	-32.8188586749	-9.2536500317
13	4.14740240471	-1.3982104499	0.247026337311	5.54631962193	1.45478422152	3.56132276583	0.158912455094	0.787968137308	-0.0315103042986	-0.357152904224	0.110844192457	0.202822427621	0.0272186806801	-0.173799781765	-0.182883418761	0.192856206559	-0.0418950547602	-0.0129136955962	0.375262842719	-0.00553511163156	0.14783471252	-12.1423669797	-31.7230750293	8.71403160903
14	3.68194176535	1.48033034875	1.56981197939	3.35752306151	-0.936593646289	3.27757802176	0.216967630624	-0.0954863648161	-0.306018573534	0.09837311606	0.190684269644	0.251378671017	0.227749370524	0.0879050941624	-0.31133914925	0.223883494481	0.0208454296884	-0.0433004006294	0.108842868185	0.0233049704589	0.207825114098	-1.17418089654	-36.3088652222	30.955630249
15	2.86072386473	-0.310913641827	2.36083314646	0.455527798898	0.635250637607	5.38936225622	0.0390129779763	-0.185207070692	-0.140180899757	0.126484259609	0.239832069498	0.0570673712849	0.35323899056	-0.0230376073458	-0.29016653182	0.368627570445	-0.0182285756719	-0.0825033714658	0.38070243674	0.128295296958	0.257112586962	8.96739672075	-37.2731237152	57.3361800312
16	6.37772179098	-4.96661633302	5.3594547014	5.23809345085	-5.27495973332	8.03451126797	0.651206764794	0.0522027353209	-1.19658571615	-0.40290242125	0.542889904121	1.28979096005	0.554360900908	-1.41430566094	-1.08529387367	0.343406012022	-0.0237577800604	-0.141048026986	0.51409365069	0.06365214454	0.359616278159	4.86243690533	-37.0002247487	64.2191033812
17	3.76050029207	-0.690057683212	4.42002120862	1.19463110972	-1.78359060316	6.50807065863	0.229737059122	-0.360651731116	-0.422388784804	0.0432510411139	0.114060468059	0.0409762784976	0.365898208851	-0.553871148592	-0.34330203464	0.269618786687	-0.0226359684916	-0.023795574441	0.194943293671	0.0292772200184	0.20965855077	1.48517231998	-37.1708307362	39.2594752929

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'D' and (resid 16 through 25 )
2	X-RAY DIFFRACTION	2	chain 'D' and (resid 26 through 28 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 1 through 39 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 40 through 116 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 117 through 161 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1 through 20 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 21 through 39 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 40 through 51 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 52 through 116 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 117 through 140 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 141 through 160 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 1 through 5 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 6 through 10 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 11 through 20 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 21 through 28 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 1 through 5 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 6 through 15 )

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