PDB-7l6l: Crystal Structure of the DNA-binding Transcriptional Repressor De...

ID or keywords:

Entry

Database: PDB / ID: 7l6l

Title

Crystal Structure of the DNA-binding Transcriptional Repressor DeoR from Escherichia coli str. K-12

Components

Deoxyribose operon repressor

Keywords

DNA BINDING PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / DNA-binding / Transcriptional Repressor

Function / homology

Function and homology information

negative regulation of DNA-templated transcription initiation / cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.75 Å

Authors

Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Wiersum, G. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: Crystal Structure of the DNA-binding Transcriptional Repressor DeoR from Escherichia coli str. K-12.
Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Wiersum, G. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Dec 23, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 1, 2021	Provider: repository / Type: Initial release
Revision 1.1	Nov 6, 2024	Group: Data collection / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7l6l.cif.gz	469 KB	Display	PDBx/mmCIF format
PDB format	pdb7l6l.ent.gz	388.8 KB	Display	PDB format
PDBx/mmJSON format	7l6l.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7l6l_validation.pdf.gz	485 KB	Display	wwPDB validaton report
Full document	7l6l_full_validation.pdf.gz	489.7 KB	Display
Data in XML	7l6l_validation.xml.gz	54.3 KB	Display
Data in CIF	7l6l_validation.cif.gz	79.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l6/7l6l ftp://data.pdbj.org/pub/pdb/validation_reports/l6/7l6l	HTTPS FTP

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Related structure data

Similar structure data	5y58-1 4edq-d 5y58-2 3h4m-d 4zhx-2 12723 5a6j-3 5fl2-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: CSGID-IDP96077

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Deoxyribose operon repressor

B: Deoxyribose operon repressor

C: Deoxyribose operon repressor

D: Deoxyribose operon repressor

E: Deoxyribose operon repressor

F: Deoxyribose operon repressor

hetero molecules

130 kDa, 6 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)	70.751, 64.734, 140.710
Angle α, β, γ (deg.)	90.000, 97.940, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Deoxyribose operon repressor Mass: 21243.820 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: deoR, nucR, b0840, JW0824 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): magic / References: UniProt: P0ACK5
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1235 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.54 Å³/Da / Density % sol: 51.6 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop Details: Protein: 3.0 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3, 5% Glycerol, TEV; Screen: Classics II (G5), 0.2M Lithium sulfate, 0.1M Tris pH 8.5, 25% (w/v) PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 17, 2019 / Details: Be
Radiation	Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 1.75→30 Å / Num. obs: 127632 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / B_iso Wilson estimate: 24.5 Å² / R_merge(I) obs: 0.07 / R_pim(I) all: 0.036 / R_rim(I) all: 0.079 / R_sym value: 0.07 / Χ²: 1.348 / Net I/σ(I): 24
Reflection shell	Resolution: 1.75→1.78 Å / Redundancy: 4.8 % / R_merge(I) obs: 0.781 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 6297 / CC_1/2: 0.814 / CC star: 0.947 / R_pim(I) all: 0.393 / R_rim(I) all: 0.876 / R_sym value: 0.781 / Χ²: 1.006 / % possible all: 99.4

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
PDB_EXTRACT	3.25	data extraction
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.75→29.7 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.964 / SU B: 4.571 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1832	6304	5 %	RANDOM
R_work	0.158	-	-	-
obs	0.1593	120563	99.71 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 108.5 Å² / B_iso mean: 28.471 Å² / B_iso min: 15.05 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.61 Å²	0 Å²	1.71 Å²
2-	-	-0.71 Å²	0 Å²
3-	-	-	-1.32 Å²

Refinement step

Cycle: final / Resolution: 1.75→29.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8583	0	121	1309	10013
B_iso mean	-	-	46.49	39.11	-
Num. residues	-	-	-	-	1078

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	9100
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	8341
X-RAY DIFFRACTION	r_angle_refined_deg	1.346	1.649	12366
X-RAY DIFFRACTION	r_angle_other_deg	0.371	1.575	19395
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.481	5	1122
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	26.728	22.43	461
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.039	15	1466
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	7.332	15	48
X-RAY DIFFRACTION	r_chiral_restr	0.063	0.2	1177
X-RAY DIFFRACTION	r_gen_planes_refined	0.052	0.02	10163
X-RAY DIFFRACTION	r_gen_planes_other	0.047	0.02	1957

LS refinement shell

Resolution: 1.75→1.795 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.277	499	-
R_work	0.251	8747	-
all	-	9246	-
obs	-	-	99.38 %

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	8.6423	2.2177	-1.3246	2.7321	-0.4486	4.1248	0.1608	-0.1673	0.2511	0.0913	-0.0162	0.161	-0.2959	0.15	-0.1447	0.1065	0.0096	0.0332	0.0181	0.0077	0.0509	53.1609	46.8192	20.9976
2	2.9411	0.8027	-1.0528	2.6457	-0.9666	2.0899	0.1541	0.0677	0.235	0.1202	0.0695	0.2878	-0.3047	-0.2094	-0.2236	0.0532	0.0426	0.0176	0.0627	0.0306	0.1026	44.2215	34.9755	27.608
3	1.4884	-0.0173	0.1862	1.4729	-0.3099	1.0078	0.0833	-0.1779	0.1543	0.008	0.025	0.0149	-0.1937	0.0593	-0.1083	0.0907	-0.01	0.0033	0.1254	0.0132	0.097	55.4715	30.4383	35.1105
4	8.9107	-0.0358	0.5959	0.8691	0.521	0.3552	-0.0665	0.0598	-0.329	0.0212	0.0678	0.0357	0.0109	0.0478	-0.0013	0.0949	0.0238	0.0256	0.105	0.0262	0.0445	55.4699	16.7076	32.7153
5	1.1061	0.0298	-0.8438	1.1711	-0.0115	1.4373	0.0224	0.1116	0.0156	-0.1212	0.0006	0.0469	-0.016	-0.0889	-0.023	0.0593	-0.0003	-0.0113	0.0526	0.0113	0.0634	56.0025	28.658	18.1301
6	2.6793	0.6656	-1.438	5.2244	-0.0464	3.0045	-0.0713	0.6059	0.0225	-0.5808	0.1964	0.349	0.0961	-0.4518	-0.1251	0.1296	-0.0104	-0.079	0.1865	0.0224	0.0576	47.9939	32.2482	7.8986
7	7.4396	3.001	0.6944	12.0975	-0.9698	3.353	-0.1331	0.0635	-0.3319	-0.171	0.2998	0.78	0.043	-0.3127	-0.1667	0.0111	0.0042	-0.0222	0.1134	0.0389	0.1766	16.8322	10.7174	73.2401
8	1.3117	-0.3086	-0.5195	1.483	-0.5755	2.0209	-0.0104	0.1142	0.0254	-0.1243	0.0546	0.0882	0.0559	-0.1251	-0.0443	0.0291	-0.0102	-0.0444	0.0695	0.0043	0.0803	31.6487	17.3098	61.6063
9	7.5403	-0.6978	-2.5765	1.2122	-0.508	1.3677	-0.1152	-0.3424	-0.1153	-0.1322	0.0323	-0.0619	0.1453	0.1117	0.0829	0.1109	-0.0262	-0.0223	0.0431	-0.0028	0.0848	35.757	0.6927	61.117
10	3.4552	0.1152	0.3723	7.6053	-0.9894	0.1765	-0.0425	-0.016	-0.2819	0.0023	0.0472	-0.1002	0.0015	0.0049	-0.0047	0.0789	0.0105	0.0344	0.0815	0.0112	0.0867	47.5446	7.5289	58.3763
11	1.3115	0.2575	-0.5278	1.4983	-0.4485	1.6633	-0.0274	-0.1018	-0.0697	0.0245	0.0009	0.005	-0.0139	0.1023	0.0265	0.0214	0.0032	-0.0393	0.0832	-0.0086	0.0902	36.3752	9.9054	75.8727
12	5.6396	-0.1779	0.7858	2.94	-0.2618	4.8659	0.1735	-0.2991	0.0975	0.3051	-0.0527	-0.0606	-0.3684	0.141	-0.1208	0.085	-0.008	-0.0018	0.0651	-0.041	0.0388	33.8653	18.2788	87.3204
13	7.6636	5.8111	4.3977	11.6459	4.3	10.2694	0.0746	-0.0445	-0.1088	0.1876	-0.0251	-0.4703	0.0679	0.717	-0.0495	0.0236	0.048	-0.0109	0.1957	0.0215	0.0598	87.7339	-2.4189	39.0674
14	1.7833	-0.8559	0.3964	1.5398	0.0695	3.2727	-0.0065	-0.0206	-0.078	-0.0571	0.0209	-0.0522	0.2974	0.3084	-0.0144	0.0647	0.0518	-0.0113	0.0746	0.0174	0.0503	78.7709	-4.156	28.8369
15	1.0511	-0.0743	0.4804	4.3003	1.6581	1.6137	0.0871	0.0421	-0.0691	-0.1503	0.0244	-0.4219	0.0589	0.268	-0.1116	0.0525	0.0434	0.015	0.1038	0.0147	0.0611	79.9657	3.8701	21.975
16	0.5476	-0.5582	-0.1089	1.8352	-0.3577	1.14	-0.0486	-0.0913	-0.0203	0.1292	0.0411	0.0027	0.0392	0.0651	0.0075	0.0315	0.0193	-0.0267	0.0832	0.0095	0.0515	70.7864	6.3255	35.6136
17	2.9749	-0.8188	1.5616	2.3964	0.5083	4.3367	-0.0077	-0.2584	-0.0029	0.3231	0.0272	0.1016	0.267	-0.2341	-0.0195	0.0788	0.013	0.0212	0.0749	0.0436	0.0519	71.1989	-4.4356	46.1975
18	11.218	-3.1162	-3.8577	3.6203	0.3336	4.8111	0.079	-0.1011	-0.4017	0.0427	0.0495	0.2854	0.5369	-0.4487	-0.1286	0.1232	-0.0609	-0.0213	0.1016	0.0592	0.0754	68.2595	-9.228	44.5777
19	1.2923	0.6755	0.2476	3.2216	1.3337	2.0532	0.0478	-0.0047	0.2221	0.0006	0.0073	0.006	-0.2063	0.093	-0.0551	0.0409	-0.0346	-0.0095	0.1154	0.0141	0.1222	69.2415	31.5393	57.8069
20	7.7057	1.1015	-0.6088	0.9709	0.1116	1.7733	0.1308	0.2101	0.3356	0.0993	-0.0045	0.1316	-0.2453	-0.0052	-0.1263	0.0847	-0.0414	0.0024	0.0822	0.0019	0.0925	69.1803	33.6853	52.4281
21	2.0801	0.2961	-0.1832	0.7499	-0.1568	1.126	0.0512	0.0186	0.1527	0.0543	0.0165	-0.0303	-0.1359	0.0566	-0.0676	0.0275	-0.0262	-0.0074	0.081	0.0137	0.0514	61.1543	28.4385	44.0419
22	7.3308	0.4562	-0.0967	0.0384	-0.0116	0.009	-0.0646	0.028	-0.2161	-0.012	0.0374	-0.0226	0.0128	-0.016	0.0273	0.0936	-0.0216	0.0309	0.1283	-0.0165	0.094	58.7818	15.2147	41.4421
23	1.8773	0.0889	-0.8859	0.751	-0.0535	1.3784	0.0411	-0.1278	0.0698	0.0436	-0.0325	0.0272	0.0216	0.0459	-0.0086	0.0175	-0.0259	-0.0224	0.1126	-0.0065	0.0889	59.0319	21.3665	59.3169
24	3.6417	1.8507	-1.2218	4.1628	0.4517	4.6005	0.1146	-0.5692	-0.1893	0.2001	-0.1433	-0.0966	0.2334	0.4416	0.0287	0.0464	-0.0179	-0.0494	0.2168	0.0481	0.0849	67.2565	20.9476	70.1821
25	10.0708	-9.0349	-4.0113	11.2904	4.2265	5.4639	0.1265	-0.0939	0.3004	0.0325	-0.0176	-0.4194	0.0598	0.5613	-0.109	0.0354	-0.0339	-0.0021	0.1462	0.0071	0.0421	92.2244	27.6591	3.8474
26	3.5628	-0.0362	-1.0028	3.5339	0.5723	3.9441	-0.0184	-0.1324	0.0485	0.059	0.0329	-0.127	-0.1362	0.457	-0.0146	0.0406	-0.0394	-0.0079	0.0899	-0.0068	0.0102	82.4564	26.1407	10.818
27	2.4005	-1.1277	-0.0372	8.6223	5.1496	3.2695	-0.0676	-0.0695	0.1093	0.1368	0.1464	-0.158	0.0609	0.1106	-0.0788	0.0709	-0.0341	-0.0064	0.1124	-0.0138	0.0523	88.6097	29.9622	16.1605
28	1.5105	0.1794	-0.2542	2.321	-0.0454	1.8206	-0.0221	-0.0512	-0.0558	-0.0114	-0.0071	-0.1576	0.0541	0.2967	0.0292	0.0408	0.0117	0.0052	0.1004	0.0088	0.0142	79.1971	17.1273	15.8902
29	0.803	-0.3407	-0.9588	0.6297	0.3722	1.8154	0.0122	0.0864	0.0117	-0.0877	-0.0049	-0.0441	0.0406	-0.0377	-0.0073	0.0863	-0.0059	0.0107	0.0679	0.0004	0.0376	77.0059	20.9732	-0.3184
30	3.5349	-1.0196	1.0706	3.2292	-0.7153	5.6399	0.2006	0.0486	0.0663	-0.1205	-0.2088	-0.0385	-0.1655	-0.002	0.0083	0.0614	-0.019	0.0333	0.053	0.0123	0.0728	82.4871	32.0366	-9.0929
31	8.0156	-4.424	1.172	11.3267	-4.9733	5.4597	0.0789	0.0581	-0.1084	0.0662	0.1154	0.3459	0.0164	-0.5104	-0.1943	0.0067	-0.0205	0.0079	0.1398	-0.0389	0.062	25.4838	0.2245	30.0071
32	2.7481	0.8216	0.8597	2.9991	0.139	4.0334	0.1047	-0.1233	-0.3563	0.2324	-0.0652	-0.0106	0.4417	-0.4199	-0.0394	0.0951	-0.0742	0.0024	0.0657	0.0101	0.0995	34.8466	-5.308	38.2964
33	0.5998	0.4622	0.3351	4.1933	1.4679	0.9602	0.0509	-0.0781	-0.0611	0.2939	-0.0764	0.118	0.1939	-0.3033	0.0254	0.1747	-0.0715	0.002	0.1777	0.0156	0.1131	34.8226	1.284	47.6295
34	1.6604	0.4893	-0.0105	1.2728	1.6615	2.4686	0.086	-0.0092	-0.1846	-0.0167	0.0187	-0.1538	-0.0569	-0.0154	-0.1047	0.161	-0.0232	-0.022	0.1155	0.0021	0.1818	44.9077	7.0183	38.4733
35	2.1954	0.8604	0.8308	3.843	-0.1561	3.7707	-0.0805	0.2112	-0.0575	-0.2234	0.0207	-0.0923	-0.1868	-0.0261	0.0598	0.0336	-0.0126	0.0149	0.0455	-0.0247	0.0204	40.5555	6.2984	28.2073
36	5.1518	-0.1872	-0.6747	1.6282	-0.2916	4.2561	0.0617	0.4214	-0.0825	-0.2376	-0.1048	-0.0824	0.2302	-0.071	0.0431	0.0589	-0.0012	0.0256	0.0864	-0.0587	0.0819	42.0315	-1.004	21.1701

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	74 - 81
2	X-RAY DIFFRACTION	2	A	82 - 120
3	X-RAY DIFFRACTION	3	A	121 - 156
4	X-RAY DIFFRACTION	4	A	157 - 162
5	X-RAY DIFFRACTION	5	A	163 - 223
6	X-RAY DIFFRACTION	6	A	224 - 252
7	X-RAY DIFFRACTION	7	B	70 - 81
8	X-RAY DIFFRACTION	8	B	82 - 145
9	X-RAY DIFFRACTION	9	B	146 - 154
10	X-RAY DIFFRACTION	10	B	155 - 163
11	X-RAY DIFFRACTION	11	B	164 - 235
12	X-RAY DIFFRACTION	12	B	236 - 252
13	X-RAY DIFFRACTION	13	C	74 - 84
14	X-RAY DIFFRACTION	14	C	85 - 111
15	X-RAY DIFFRACTION	15	C	112 - 151
16	X-RAY DIFFRACTION	16	C	152 - 223
17	X-RAY DIFFRACTION	17	C	224 - 243
18	X-RAY DIFFRACTION	18	C	244 - 252
19	X-RAY DIFFRACTION	19	D	74 - 99
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25	X-RAY DIFFRACTION	25	E	75 - 89
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28	X-RAY DIFFRACTION	28	E	115 - 159
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30	X-RAY DIFFRACTION	30	E	229 - 252
31	X-RAY DIFFRACTION	31	F	74 - 84
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34	X-RAY DIFFRACTION	34	F	154 - 200
35	X-RAY DIFFRACTION	35	F	201 - 224
36	X-RAY DIFFRACTION	36	F	225 - 252

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