PDB-8ylm: Crystal structure of Deinococcus radiodurans HucR in complex with...

ID or keywords:

Entry

Database: PDB / ID: 8ylm

Title

Crystal structure of Deinococcus radiodurans HucR in complex with uric acid

Components

Transcriptional regulator, MarR family

Keywords

TRANSCRIPTION / Transcription factor

Function / homology

Function and homology information

response to stress / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function

Biological species

Deinococcus radiodurans (radioresistant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 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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Download

PDBx/mmCIF format	8ylm.cif.gz	259 KB	Display	PDBx/mmCIF format
PDB format	pdb8ylm.ent.gz	208 KB	Display	PDB format
PDBx/mmJSON format	8ylm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yl/8ylm ftp://data.pdbj.org/pub/pdb/validation_reports/yl/8ylm	HTTPS FTP

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Related structure data

Related structure data	8ylfSC 8ylgC 8ylhC 8yliC 8yljC 8ylkC 8yllC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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

Deposited unit

A: Transcriptional regulator, MarR family

B: Transcriptional regulator, MarR family

C: Transcriptional regulator, MarR family

D: Transcriptional regulator, MarR family

hetero molecules

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

1

A: Transcriptional regulator, MarR family

B: Transcriptional regulator, MarR family

hetero molecules

defined by author&software
Evidence: gel filtration
40.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Transcriptional regulator, MarR family

D: Transcriptional regulator, MarR family

hetero molecules

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

Unit cell

Length a, b, c (Å)	56.815, 57.206, 60.511
Angle α, β, γ (deg.)	67.26, 80.25, 79.90
Int Tables number	1
Space group name H-M	P1
Symmetry operation	#1: x,y,z

#1: Protein	Transcriptional regulator, MarR family Mass: 20204.969 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans (radioresistant) Gene: DR_1159 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9RV71
#2: Chemical	ChemComp-URC / URIC ACID / 7,9-DIHYDRO-1H-PURINE-2,6,8(3H)-TRIONE Mass: 168.110 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C₅H₄N₄O₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 2.2 Å³/Da / Density % sol: 43.98 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: PEG 1000, Tris

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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: Jul 22, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 1.95→30 Å / Num. obs: 48572 / % possible obs: 97.1 % / Redundancy: 2 % / CC_1/2: 0.996 / Net I/σ(I): 17.6
Reflection shell	Resolution: 1.95→1.98 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2393 / CC_1/2: 0.623 / % possible all: 95.9

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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: 8YLF

8ylf

Resolution: 1.95→29.377 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 24.32 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2286	2498	5.15 %
R_work	0.1906	-	-
obs	0.1926	48542	96.87 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.95→29.377 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4731	0	48	364	5143

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4856
X-RAY DIFFRACTION	f_angle_d	0.886	6606
X-RAY DIFFRACTION	f_dihedral_angle_d	9.057	3015
X-RAY DIFFRACTION	f_chiral_restr	0.049	804
X-RAY DIFFRACTION	f_plane_restr	0.006	844

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 (%)
1.95-1.9875	0.3461	117	0.2769	2432	X-RAY DIFFRACTION	92
1.9875-2.0281	0.2853	138	0.2483	2562	X-RAY DIFFRACTION	96
2.0281-2.0722	0.3058	110	0.2296	2551	X-RAY DIFFRACTION	97
2.0722-2.1204	0.2921	153	0.2167	2545	X-RAY DIFFRACTION	96
2.1204-2.1734	0.2584	161	0.1982	2531	X-RAY DIFFRACTION	97
2.1734-2.2321	0.2375	131	0.1911	2560	X-RAY DIFFRACTION	97
2.2321-2.2978	0.251	148	0.1932	2560	X-RAY DIFFRACTION	97
2.2978-2.3719	0.2424	134	0.1879	2581	X-RAY DIFFRACTION	97
2.3719-2.4566	0.237	134	0.1889	2529	X-RAY DIFFRACTION	97
2.4566-2.5549	0.2214	123	0.1893	2605	X-RAY DIFFRACTION	97
2.5549-2.6712	0.1806	128	0.194	2575	X-RAY DIFFRACTION	97
2.6712-2.8119	0.243	144	0.1931	2583	X-RAY DIFFRACTION	97
2.8119-2.9879	0.2798	138	0.2076	2612	X-RAY DIFFRACTION	98
2.9879-3.2183	0.2418	129	0.2092	2570	X-RAY DIFFRACTION	98
3.2183-3.5417	0.2416	151	0.1917	2576	X-RAY DIFFRACTION	98
3.5417-4.0531	0.183	150	0.1688	2587	X-RAY DIFFRACTION	98
4.0531-5.1021	0.2102	167	0.1571	2571	X-RAY DIFFRACTION	98
5.1021-29.377	0.1849	142	0.1788	2514	X-RAY DIFFRACTION	96

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	2.8252	-0.5475	-0.2428	0.8981	-0.9017	1.8981	-0.0137	-0.1609	0.1704	0.0547	0.187	0.1847	-0.1099	-0.2507	-0.1297	0.1298	0.0079	0.0077	0.1513	-0.0213	0.1917	-20.0821	53.1295	33.6385
2	5.9475	-2.7666	-1.2056	9.3234	0.6945	2.3069	-0.065	0.1991	0.0303	0.0586	0.0737	0.7251	-0.1601	-0.6952	0.0255	0.2463	0.0478	0.0448	0.423	-0.0096	0.2231	-48.9684	3.1392	3.727
3	1.415	-0.2122	-0.7209	1.2167	-0.4395	2.169	0.0064	-0.3163	0.0108	0.0745	-0.087	-0.2846	-0.0324	0.4457	0.0693	0.1385	-0.0234	-0.0284	0.2139	-0.0221	0.2001	-20.646	-2.8841	-7.4947
4	2.7183	0.6069	-0.4724	1.0032	-0.2686	0.8799	0.1077	-0.2105	1.1701	0.2871	-0.3788	-0.658	-0.2829	0.5316	0.1055	0.215	-0.0561	-0.1019	0.4754	0.0379	0.6205	-8.1977	2.0585	-10.1602
5	3.1656	-0.5179	-0.9001	1.3582	-0.4891	1.4961	-0.0755	0.0228	-0.0701	-0.0302	-0.1279	-0.1749	0.0639	0.0696	0.1586	0.1145	0.0094	0.0034	0.1965	-0.013	0.1561	-26.2261	-11.1239	-9.4835
6	4.019	-1.8559	-1.4656	4.4247	0.2014	4.9126	0.1799	0.1676	-0.0428	-0.6351	-0.2204	-0.466	0.4696	0.0647	0.0715	0.1844	-0.0023	0.0379	0.2027	-0.0071	0.2086	-20.3476	-10.0331	-20.1557
7	1.5986	-0.6467	-1.0463	1.8902	0.6305	2.9991	0.1771	-0.0031	0.3258	-0.0888	0.091	-0.2534	-0.5598	-0.0016	-0.29	0.1816	-0.0026	-0.0022	0.1919	0.0055	0.2048	-32.9058	4.8429	-5.5451
8	1.9832	1.7023	0.7257	3.8494	1.1184	4.7555	-0.4453	-0.2455	0.3657	0.3307	0.4978	-0.6174	-0.7064	0.0567	-0.0663	0.4165	0.1265	-0.0214	0.3095	-0.0909	0.3443	-37.4233	11.5166	12.3931
9	1.1522	-0.9092	-0.1907	1.8425	0.0058	2.5166	-0.1212	0.0186	0.2354	0.3325	0.2553	0.0387	-0.5759	-0.428	0.0074	0.2946	0.1153	0.0314	0.2107	0.0018	0.2135	-42.3811	6.9092	-2.0453
10	3.4446	2.1769	-4.9242	2.9442	-2.7748	9.4106	0.0401	-0.1052	0.5394	0.1761	-0.1069	-0.3396	-0.5787	0.1993	0.2204	0.2114	0.0147	-0.0878	0.2194	-0.0102	0.3254	-24.8499	61.9176	26.6478
11	5.1149	-4.8357	-4.7092	5.7165	5.08	5.7393	0.0331	0.2802	-0.1099	-0.2854	-0.2363	0.1915	-0.0476	-0.1982	0.1881	0.1543	-0.0173	-0.0094	0.1481	-0.0036	0.1383	-16.2391	48.54	22.3043
12	2.6315	1.1126	-0.3933	1.9726	0.0919	5.4541	0.0856	0.1383	-0.3943	-0.4387	-0.149	0.0488	0.099	0.1272	0.0626	0.2518	0.0399	0.0265	0.1469	-0.0688	0.1932	-5.6584	26.9794	20.0532
13	1.2531	2.0645	1.3244	6.1823	1.3727	4.4749	0.0116	-0.0159	-0.5217	-0.0935	-0.4108	1.4843	0.2661	-1.1044	0.5463	0.2864	-0.0164	-0.0392	0.3291	-0.1386	0.5419	-14.7135	25.9438	20.472
14	5.602	-0.8478	-1.2882	2.971	3.1329	3.529	-0.1792	0.0745	-0.7084	0.1597	-0.1882	0.4796	0.8032	-0.0182	-0.3019	0.5662	0.0665	-0.0918	0.1896	-0.1878	0.3689	-7.5564	16.87	15.0819
15	5.2105	-1.5412	2.3688	7.353	-3.8798	3.8744	-0.0461	-0.1049	0.0621	-0.921	-0.3653	-0.6084	0.7342	0.6464	0.4123	0.6272	0.092	0.0996	0.5177	-0.0521	0.4054	-6.4355	5.6159	25.3335
16	1.262	-0.5195	-0.2627	0.6766	0.8149	1.1397	0.0274	0.3146	-0.116	-0.6111	-0.0727	-0.2505	0.2486	0.0587	0.0566	0.3938	0.0374	0.0525	0.2213	-0.0228	0.1518	-2.4494	32.9746	13.1027
17	4.566	1.4172	-4.2766	2.1783	-3.8539	9.3966	-0.0926	-0.2455	-0.0514	-0.0506	-0.1456	-0.2537	0.1194	0.4355	0.2722	0.1435	0.0108	-0.0204	0.0972	-0.0314	0.2	-4.2072	48.892	31.989
18	8.972	-1.1949	-5.9924	7.2967	0.0592	7.48	0.0182	-0.0924	0.2449	-0.1054	0.0907	-0.3978	-0.2712	0.6301	-0.0017	0.2073	-0.0296	-0.0417	0.2013	-0.0394	0.2368	2.8753	34.7677	26.8571
19	3.1223	-1.7471	0.2958	1.8663	-0.6372	0.6614	0.0886	-0.1672	-0.3241	-0.0664	0.1054	0.3197	0.1181	-0.1739	-0.2094	0.1743	-0.0443	-0.0219	0.1697	-0.0305	0.1779	-25.7663	47.7929	27.2907
20	4.4735	0.0587	-0.8503	4.9898	0.0368	1.4666	0.5269	0.6837	-1.2214	-0.6873	0.0121	0.6944	0.5428	-0.6485	-0.1902	0.3443	-0.0837	-0.1758	0.4489	0.0015	0.506	-40.287	49.2616	20.0951

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 134 through 179 )
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 7 through 38 )
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 39 through 95 )
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 96 through 133 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 134 through 179 )
6	X-RAY DIFFRACTION	6	chain 'D' and (resid 7 through 25 )
7	X-RAY DIFFRACTION	7	chain 'D' and (resid 26 through 81 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 82 through 112 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 113 through 179 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 5 through 38 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 39 through 61 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 62 through 95 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 96 through 112 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 113 through 120 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 121 through 127 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 128 through 155 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 156 through 179 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 7 through 38 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 39 through 95 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 96 through 133 )

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