PDB-5f7q: ROK repressor Lmo0178 from Listeria monocytogenes bound to operator

ID or keywords:

Entry

Database: PDB / ID: 5f7q

Title

ROK repressor Lmo0178 from Listeria monocytogenes bound to operator

Components

(Operator) x 2
Lmo0178 protein

Keywords

TRANSCRIPTION/DNA / repressor / open reading frame / kinase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / TRANSCRIPTION-DNA complex

Function / homology

Function and homology information

metal ion binding
Similarity search - Function

Biological species

Listeria monocytogenes serovar 1/2a (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Light, S.H. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: Nat Microbiol / Year: 2016
Title: Structure to function of an alpha-glucan metabolic pathway that promotes Listeria monocytogenes pathogenesis.
Authors: Light, S.H. / Cahoon, L.A. / Halavaty, A.S. / Freitag, N.E. / Anderson, W.F.

History

Deposition	Dec 8, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 7, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 23, 2016	Group: Database references
Revision 1.2	Sep 27, 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	5f7q.cif.gz	701.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5f7q.ent.gz	578.4 KB	Display	PDB format
PDBx/mmJSON format	5f7q.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/f7/5f7q ftp://data.pdbj.org/pub/pdb/validation_reports/f7/5f7q	HTTPS FTP

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Related structure data

Related structure data	4kmqC 5do8C 5f7pC 5f7rSC 5f7sC 5f7uC 5f7vC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3sqm-d 5wai-d 9654 9653 5c2w-d 6wqo-d 6ah8-d 21549 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
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PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

C: Lmo0178 protein

E: Lmo0178 protein

F: Operator

J: Lmo0178 protein

K: Operator

L: Lmo0178 protein

hetero molecules

203 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)	73.672, 180.257, 79.860
Angle α, β, γ (deg.)	90.00, 89.97, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 4 molecules CEJL

#1: Protein	Lmo0178 protein / Rok repressor Mass: 45366.551 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria) Strain: ATCC BAA-679 / EGD-e / Gene: lmo0178 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8YAF1

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DNA chain , 2 types, 2 molecules FK

#2: DNA chain	Operator Mass: 9533.195 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria)
#3: DNA chain	Operator Mass: 9524.181 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria)

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Non-polymers , 6 types, 291 molecules

#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Formula: Zn
#5: Chemical	ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE Mass: 178.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₈H₁₈O₄
#6: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#7: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#8: Chemical	ChemComp-7PE / 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL / POLYETHYLENE GLYCOL FRAGMENT Mass: 310.384 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₃₀O₇
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.69 Å³/Da / Density % sol: 54.23 %
Crystal grow	Temperature: 300 K / Method: vapor diffusion, sitting drop Details: 7.5 mg/mL protein in 0.5 M sodium chloride, 0.01 M Tris-HCl, pH 8.3 against Classics II H6 (Qiagen, 0.2 M sodium formate, 20% w/v PEG3350)

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 20, 2015
Radiation	Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 2.4→30 Å / Num. obs: 81757 / % possible obs: 100 % / Redundancy: 5.5 % / R_merge(I) obs: 0.067 / Net I/σ(I): 28.7
Reflection shell	Resolution: 2.4→2.44 Å / Redundancy: 5.5 % / R_merge(I) obs: 0.71 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0135	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5F7R

5f7r

Resolution: 2.4→30 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.946 / SU B: 14.68 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.364 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.218	4010	4.9 %	RANDOM
R_work	0.182	-	-	-
obs	0.184	77556	99.6 %	-

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 mean: 58.79 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.1 Å²	0 Å²	-0.33 Å²
2-	-	1.13 Å²	0 Å²
3-	-	-	-1.23 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12220	1394	163	273	14050

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.018	14239
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	13030
X-RAY DIFFRACTION	r_angle_refined_deg	1.453	1.87	19443
X-RAY DIFFRACTION	r_angle_other_deg	0.955	3.001	30050
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.165	5.064	1572
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.465	24.759	580
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.384	15	2237
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.913	15	65
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	2076
X-RAY DIFFRACTION	r_gen_planes_refined	0.023	0.02	15026
X-RAY DIFFRACTION	r_gen_planes_other	0.018	0.02	3173
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.991	3.885	6261
X-RAY DIFFRACTION	r_mcbond_other	1.991	3.884	6260
X-RAY DIFFRACTION	r_mcangle_it	3.088	5.818	7821
X-RAY DIFFRACTION	r_mcangle_other	3.088	5.818	7822
X-RAY DIFFRACTION	r_scbond_it	2.655	4.353	7978
X-RAY DIFFRACTION	r_scbond_other	2.655	4.353	7979
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.184	6.377	11623
X-RAY DIFFRACTION	r_long_range_B_refined	6.005	18.033	16155
X-RAY DIFFRACTION	r_long_range_B_other	6.005	18.034	16156
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.39→2.46 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.28	304	-
R_work	0.24	5487	-
obs	-	-	95.72 %

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	1.6431	-0.2205	-1.4767	3.2024	-0.1844	2.2362	0.1583	-0.1772	-0.0904	0.3647	-0.2491	0.3271	-0.1187	0.1931	0.0908	0.0988	-0.0688	0.1012	0.0597	-0.0418	0.2299	72.8966	-13.8799	112.1334
2	0.8016	0.4859	-0.52	10.0116	3.3965	2.3409	0.0573	-0.1323	-0.0444	0.2845	-0.2163	0.3554	0.2361	-0.2015	0.1589	0.0746	-0.0805	0.0408	0.1195	0.0222	0.1646	64.5221	-42.9109	115.578
3	3.0644	0.2052	0.225	4.977	0.0879	3.7509	-0.1204	0.056	-0.0033	0.2607	0.0465	0.5272	0.3593	-0.4853	0.074	0.086	-0.0909	0.0125	0.1255	0.0276	0.2286	64.6694	-46.3209	106.6954
4	3.1092	0.4957	-0.326	0.9891	0.2378	1.7264	0.0477	-0.0248	0.1089	-0.023	0.0389	0.1808	0.0204	0.039	-0.0866	0.0208	-0.0016	-0.0047	0.0081	0.0124	0.0532	78.0482	-41.5364	108.8783
5	1.6495	-0.2529	0.4016	1.6204	-0.9662	6.0623	-0.0399	-0.2799	-0.5055	-0.2994	0.0282	0.1015	0.571	-0.5581	0.0117	0.1176	-0.0148	-0.027	0.1269	0.0678	0.2459	88.4944	-63.7942	118.2384
6	1.5661	-0.1317	-0.2664	1.0699	-0.7244	0.8175	0.0916	-0.4203	-0.0464	0.1479	-0.0145	0.048	-0.0198	0.1548	-0.0772	0.0782	-0.0188	-0.0089	0.1562	-0.0166	0.0396	88.3633	-43.53	117.1051
7	2.0754	-0.499	-1.5178	2.3356	-0.5888	4.9947	-0.0221	0.1523	-0.2011	-0.3266	-0.3	0.1509	0.1427	-0.2585	0.3221	0.1278	0.0711	0.0114	0.0988	-0.0905	0.1877	84.4793	-16.4498	81.0713
8	6.6524	-1.0623	3.7115	1.2042	0.013	3.613	0.1748	-0.006	0.1146	-0.091	0.0211	-0.11	-0.0769	0.1771	-0.1959	0.0769	0.0181	0.0983	0.1665	-0.017	0.139	113.9619	-25.7705	89.858
9	2.8798	1.015	0.0556	1.6949	-0.3778	1.564	0.1765	-0.1832	0.2468	-0.0858	-0.0379	-0.0852	-0.1335	0.0301	-0.1386	0.0746	0.0371	0.0633	0.1756	-0.0575	0.1262	105.3996	-29.6896	96.159
10	2.2496	-1.432	-0.2982	3.1869	-0.8542	1.2816	0.0393	-0.1914	-0.0515	-0.103	-0.1171	-0.2511	0.2308	0.4631	0.0777	0.0792	0.0858	-0.0097	0.2601	0.0242	0.1124	108.1592	-48.9476	106.0223
11	3.8338	-0.6635	-0.2003	0.7564	-0.384	2.0977	0.1084	0.4379	-0.3245	-0.3657	-0.1949	-0.1079	0.3103	0.3565	0.0866	0.2104	0.1178	0.0526	0.1669	-0.0557	0.1115	105.9922	-56.5261	93.8425
12	1.0647	1.0266	-0.8611	1.9976	-1.0478	1.2969	0.2217	0.268	0.2048	-0.1385	0.0305	-0.1058	-0.0051	0.0732	-0.2522	0.2689	0.1053	0.0692	0.3845	-0.0152	0.3198	99.4202	-30.4435	90.2294
13	5.9474	2.2709	4.1316	7.1104	-2.0018	4.9304	-0.2948	-0.2773	-0.0549	0.1716	0.4349	0.0524	-0.3856	-0.4775	-0.1401	0.3728	-0.0824	0.1452	0.3645	-0.1651	0.2327	71.4026	12.6753	134.0777
14	0.3316	0.1531	-0.1733	2.1214	0.0132	3.9911	0.2448	0.0379	0.0565	-0.0813	-0.2534	0.3811	0.0127	-0.3614	0.0086	0.1944	0.0414	-0.0062	0.1104	-0.101	0.2615	72.6164	-1.5959	98.0721
15	7.2025	-3.7789	-2.7679	4.2729	2.6961	6.9313	0.0596	0.858	0.2461	-0.6183	-0.0557	-0.1325	0.0374	-0.2233	-0.0039	0.4115	0.0427	-0.0458	0.3591	-0.0916	0.0959	73.8687	-9.6176	62.465
16	1.9512	0.2761	1.6057	2.1661	-0.7348	4.9173	-0.0724	-0.1299	0.1922	0.3108	-0.2483	0.1277	-0.189	-0.1743	0.3207	0.1308	-0.0656	0.0197	0.0698	-0.0794	0.1749	84.5396	15.5875	118.2807
17	6.4901	1.4816	-3.4457	1.5652	-0.177	2.7748	0.1929	-0.0623	-0.1834	0.0976	0.0154	-0.1448	0.0771	0.1854	-0.2082	0.059	-0.012	-0.0813	0.1731	-0.0276	0.1255	113.9706	24.801	109.7927
18	2.9429	-0.9249	0.0088	1.5046	-0.3315	1.5933	0.1968	0.2053	-0.2425	0.0843	-0.0514	-0.0607	0.1191	0.0215	-0.1454	0.0716	-0.0393	-0.0283	0.1738	-0.048	0.1135	105.2719	28.8041	103.4726
19	2.2859	1.2833	0.7113	2.9776	0.2611	1.8161	0.007	-0.0377	0.1729	0.2078	-0.1177	-0.3367	-0.3478	0.6466	0.1107	0.1388	-0.1617	-0.0028	0.3615	0.0404	0.1783	112.8785	53.8141	98.991
20	1.896	-0.6269	0.0985	1.9293	-1.2116	2.3313	-0.0244	-0.44	0.3711	0.5393	-0.0561	-0.1326	-0.4073	0.106	0.0805	0.2533	-0.0841	0.0251	0.2207	-0.0894	0.1334	97.3957	51.2076	107.4474
21	7.7912	4.7536	2.9641	5.1444	1.6078	1.3094	0.2412	-0.1401	-0.3994	0.0715	0.0359	-0.1551	0.0019	-0.0262	-0.2771	0.1295	-0.0424	-0.0142	0.202	0.0113	0.182	98.6711	24.9403	107.7206
22	12.4534	-0.2268	0.5107	6.816	-3.0032	5.6905	-0.1541	0.0755	-1.022	-0.3571	0.7234	-0.2177	0.4609	-0.5917	-0.5694	0.3323	0.0372	-0.0781	0.3065	-0.0744	0.2174	70.1781	-14.7523	64.3784
23	1.1005	0.4421	0.5427	2.4899	0.6646	6.2892	0.2004	-0.0409	-0.17	-0.1552	-0.2443	0.1815	-0.0557	-0.2408	0.0438	0.1079	0.0555	-0.0367	0.0889	-0.0772	0.2421	74.0604	-2.0556	92.3278
24	3.0649	0.6307	1.4605	1.1538	-1.0453	6.3592	0.0415	-0.7144	0.1448	0.5357	-0.0189	0.0248	-0.0522	-0.6451	-0.0226	0.4454	-0.0391	0.1043	0.2609	-0.1502	0.2027	72.3982	7.484	129.82
25	1.6961	-0.0388	1.1698	2.8682	-0.2197	2.8357	0.2171	0.2228	0.0906	-0.3227	-0.2641	0.3922	0.1711	0.1036	0.0471	0.1052	0.0823	-0.0672	0.0699	-0.049	0.2537	72.9363	13.1386	87.6976
26	0.3854	-0.2646	0.4282	10.3027	3.2656	2.6822	0.0134	0.1046	0.0158	-0.2918	-0.1096	0.2668	-0.2702	-0.2032	0.0962	0.0524	0.0668	-0.0333	0.133	0.0173	0.1751	64.4956	41.9427	84.0885
27	2.7492	-0.2913	0.1659	4.5984	0.3491	3.1633	-0.1198	-0.2196	0.092	-0.2015	-0.0587	0.4683	-0.3023	-0.5275	0.1784	0.0727	0.089	0.0319	0.1421	0.0094	0.2378	64.6925	45.4599	92.9841
28	1.7602	0.0412	0.2868	1.2912	-0.0952	1.0737	0.1028	-0.0238	0.0296	0.0707	-0.0006	0.0961	-0.0914	-0.0307	-0.1022	0.0599	0.0164	0.0551	0.0698	-0.0044	0.0857	81.0228	45.423	90.951
29	2.4579	-0.8904	-0.0995	4.3312	-0.6675	7.3414	0.0342	0.1808	0.3603	0.2143	0.1138	0.2545	-0.73	-0.3701	-0.1479	0.1089	-0.008	0.0489	0.2198	0.1374	0.2518	88.5742	63.3244	75.5507
30	1.761	0.2186	0.1998	0.7621	-0.7114	1.3147	0.0704	0.47	0.0178	-0.1636	-0.022	0.0327	-0.0174	0.1524	-0.0484	0.1319	0.0292	0.0383	0.1625	-0.0322	0.1096	87.7647	41.3106	82.803

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	C	3 - 76
2	X-RAY DIFFRACTION	2	C	77 - 120
3	X-RAY DIFFRACTION	3	C	121 - 170
4	X-RAY DIFFRACTION	4	C	171 - 243
5	X-RAY DIFFRACTION	5	C	244 - 310
6	X-RAY DIFFRACTION	6	C	311 - 397
7	X-RAY DIFFRACTION	7	E	3 - 76
8	X-RAY DIFFRACTION	8	E	77 - 132
9	X-RAY DIFFRACTION	9	E	133 - 230
10	X-RAY DIFFRACTION	10	E	231 - 277
11	X-RAY DIFFRACTION	11	E	278 - 367
12	X-RAY DIFFRACTION	12	E	368 - 397
13	X-RAY DIFFRACTION	13	F	2 - 8
14	X-RAY DIFFRACTION	14	F	9 - 24
15	X-RAY DIFFRACTION	15	F	25 - 30
16	X-RAY DIFFRACTION	16	J	2 - 76
17	X-RAY DIFFRACTION	17	J	77 - 132
18	X-RAY DIFFRACTION	18	J	133 - 231
19	X-RAY DIFFRACTION	19	J	232 - 317
20	X-RAY DIFFRACTION	20	J	318 - 375
21	X-RAY DIFFRACTION	21	J	376 - 397
22	X-RAY DIFFRACTION	22	K	2 - 7
23	X-RAY DIFFRACTION	23	K	8 - 19
24	X-RAY DIFFRACTION	24	K	20 - 30
25	X-RAY DIFFRACTION	25	L	2 - 76
26	X-RAY DIFFRACTION	26	L	77 - 120
27	X-RAY DIFFRACTION	27	L	121 - 170
28	X-RAY DIFFRACTION	28	L	171 - 267
29	X-RAY DIFFRACTION	29	L	268 - 317
30	X-RAY DIFFRACTION	30	L	318 - 397

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