PDB-3f8f: Crystal structure of multidrug binding transcriptional regulator ...

ID or keywords:

Entry

Database: PDB / ID: 3f8f

Title

Crystal structure of multidrug binding transcriptional regulator LmrR complexed with Daunomycin

Components

Transcriptional regulator, PadR-like family

Keywords

TRANSCRIPTION REGULATOR / Winged helix turn helix

Function / homology

Function and homology information

: / Transcription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology

Biological species

Lactococcus lactis subsp. cremoris (lactic acid bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.2 Å

Authors

Madoori, P.K. / Agustiandari, H. / Driessen, A.J.M. / Thunnissen, A.-M.W.H.

Citation

Journal: Embo J. / Year: 2009
Title: Structure of the transcriptional regulator LmrR and its mechanism of multidrug recognition.
Authors: Madoori, P.K. / Agustiandari, H. / Driessen, A.J. / Thunnissen, A.M.

History

Deposition	Nov 12, 2008	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Dec 30, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2	Apr 9, 2014	Group: Database references
Revision 1.3	Nov 1, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3f8f.cif.gz	62.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3f8f.ent.gz	46.1 KB	Display	PDB format
PDBx/mmJSON format	3f8f.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3f8f_validation.pdf.gz	801.7 KB	Display	wwPDB validaton report
Full document	3f8f_full_validation.pdf.gz	805 KB	Display
Data in XML	3f8f_validation.xml.gz	11 KB	Display
Data in CIF	3f8f_validation.cif.gz	14.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f8/3f8f ftp://data.pdbj.org/pub/pdb/validation_reports/f8/3f8f	HTTPS FTP

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Related structure data

Related structure data	3f8bSC 3f8cC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1hlz-d 6omo-d 1ga5-2 3f8c-1 1z5y-d 6vwe-d 1puj-d 6i8n-d 3w9g-3 3fpt-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Transcriptional regulator, PadR-like family

B: Transcriptional regulator, PadR-like family

hetero molecules

30.1 kDa, 2 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)	35.450, 53.025, 147.116
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	LYS	LYS	ASP	ASP	A	A	6 - 69	6 - 69
2	1	LYS	LYS	ASP	ASP	B	B	6 - 69	6 - 69
1	2	ARG	ARG	LYS	LYS	A	A	76 - 110	76 - 110
2	2	ARG	ARG	LYS	LYS	B	B	76 - 110	76 - 110

#1: Protein	Transcriptional regulator, PadR-like family / transcription regulator LmrR Mass: 14764.789 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis subsp. cremoris (lactic acid bacteria) Strain: MG1363 / Gene: lmrR / Plasmid: pNSC8048 / Production host: Lactococcus lactis (lactic acid bacteria) / Strain (production host): NZ9000 / References: UniProt: A2RI36
#2: Chemical	ChemComp-DM1 / DAUNOMYCIN / DAUNORUBICIN Mass: 527.520 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₇H₂₉NO₁₀
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.34 Å³/Da / Density % sol: 47.46 % / Mosaicity: 0.57 °
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 25% PEG1500, 0.1M malonic acid/imidazol/boric (MIB) buffer, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.92 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 9, 2006 / Details: mirrors
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.92 Å / Relative weight: 1
Reflection	Resolution: 2.2→49.884 Å / Num. all: 14655 / Num. obs: 14655 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / R_merge(I) obs: 0.071 / Net I/σ(I): 6.6
Reflection shell	Resolution: 2.2→2.32 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.273 / Mean I/σ(I) obs: 2.7 / Num. measured all: 7225 / Num. unique all: 2074 / R_sym value: 0.273 / % possible all: 99.9

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

R_factor: 54.51 / Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.1 Å	73.63 Å
Translation	2.1 Å	73.63 Å

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA	3.2.25	data scaling
PHASER		phasing
REFMAC		refinement
PDB_EXTRACT	3.006	data extraction
ADSC	Quantum 315	data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3F8B

3f8b

Resolution: 2.2→49.88 Å / Cor.coef. F_o:F_c: 0.92 / Cor.coef. F_o:F_c free: 0.886 / WR_factor R_free: 0.273 / WR_factor R_work: 0.219 / FOM work R set: 0.812 / SU B: 13.402 / SU ML: 0.171 / SU R Cruickshank DPI: 0.273 / SU R_free: 0.227 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.289 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: AUTHOR CHECKED USING MOLPROBITY AND IN COOT FOR TORSION ANGLES OUTSIDE AND ALL RESIDUES ARE WITHIN THE ALLOWED CONFORMATIONS. THERE ARE NO OUTLIERS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2796	762	5.2 %	RANDOM
R_work	0.23205	-	-	-
obs	0.23465	13853	100 %	-
all	-	14615	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso max: 109.23 Å² / B_iso mean: 24.347 Å² / B_iso min: 4.98 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.78 Å²	0 Å²	0 Å²
2-	-	3.32 Å²	0 Å²
3-	-	-	-1.54 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→49.88 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1832	0	38	43	1913

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	1899
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	0.651	1.988	2552
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.729	5	222
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.087	24.681	94
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.916	15	371
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.174	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.063	0.2	272
X-RAY DIFFRACTION	r_gen_planes_refined	0.001	0.02	1395
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.217	0.2	819
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.316	0.2	1309
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.167	0.2	75
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	0.183	0.2	53
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.166	0.2	5
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	0.684	1.5	1148
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.131	2	1771
X-RAY DIFFRACTION	r_scbond_it	1.687	3	970
X-RAY DIFFRACTION	r_scangle_it	2.798	4.5	781
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 819 / Refine-ID: X-RAY DIFFRACTION

Type	Rms dev position (Å)	Weight position
medium positional	0.77	0.5
medium thermal	0.46	2

LS refinement shell

Resolution: 2.2→2.257 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_work	0.233	1030	-
obs	-	-	100 %

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	12.2559	-6.8484	-9.8544	8.1259	6.4035	28.9968	0.0978	-0.4624	0.1925	0.2305	-0.2272	-0.1772	-0.423	0.249	0.1294	0.0765	-0.0735	0.0126	-0.0548	-0.0491	0.0968	34.538	36.2156	48.4598
2	3.2259	-0.1564	-2.9824	1.7696	1.28	5.1815	-0.1052	-0.3871	-0.0925	0.0726	0.0264	0.1886	0.4727	-0.4412	0.0788	0.0655	-0.0406	0.0081	0.2169	-0.0479	0.116	22.8049	32.8752	64.6123
3	7.1333	4.2598	5.1893	12.0382	9.0127	10.6275	0.1528	-0.4296	-0.7236	0.2825	0.0901	-0.4258	1.1231	0.6145	-0.2429	0.2109	0.043	0.0288	0.1944	0.0107	0.0491	28.6195	26.0497	63.5564
4	23.0502	-3.4355	-2.3814	9.5229	5.8092	3.5474	-0.2258	-0.3857	0.4067	0.188	0.1135	-0.4433	-0.6906	0.5167	0.1122	0.194	-0.0623	-0.0335	0.3017	0.039	0.0472	28.8923	42.7832	66.5509
5	5.5905	-0.5689	3.0539	11.7138	4.0688	5.6381	-0.1558	-0.7437	-0.0082	0.8427	0.0981	-0.6983	0.1391	-0.0733	0.0577	-0.0357	0.0213	-0.0505	0.3981	-0.0597	0.1579	21.0523	39.9395	75.6152
6	6.1911	-3.7701	1.1844	7.9094	-0.3704	16.5187	-0.4133	-0.6329	-0.5114	0.4095	0.4983	-0.3627	0.2669	0.7013	-0.0849	-0.0009	0.0389	0.0533	0.3333	-0.0262	0.1158	22.358	35.4631	77.5082
7	1.1624	0.517	-4.3532	0.2323	-1.7697	28.2425	-0.0485	-0.1893	0.3247	-0.299	-0.1586	0.1923	-0.5628	-1.3495	0.2071	0.1336	0.1046	0.0113	0.3974	-0.0444	0.2189	13.8368	43.9897	58.2011
8	1.8388	-2.0046	-1.3518	5.1804	7.0688	39.1523	-0.6057	0.0971	-0.3073	0.3226	0.1294	0.0262	0.6164	0.1169	0.4763	0.0774	0.0156	0.0325	0.1261	0.011	0.1736	15.7631	41.2808	39.0573
9	10.2095	-6.8898	13.2866	11.4264	5.6932	49.002	0.9113	0.4071	-0.2203	-1.0866	-0.1245	-0.3704	-0.5959	-1.0243	-0.7868	0.6669	-0.0353	-0.0065	0.278	-0.0067	0.2059	14.735	39.6184	22.6877
10	32.1312	-6.5764	-8.1404	37.1399	-2.2889	55.6904	0.1991	-4.0596	3.322	1.9543	-0.2923	0.5815	-1.1578	-0.4599	0.0933	0.243	-0.0196	-0.0725	0.627	-0.4894	0.3582	25.0319	48.8239	50.8369
11	3.6014	-0.753	-0.479	2.9099	-0.8491	4.505	-0.1132	0.2059	-0.0471	-0.0692	0.1533	-0.0037	-0.0926	-0.2456	-0.04	0.1392	0.0309	-0.0067	0.095	-0.0177	0.1742	26.1396	45.8743	34.1925
12	12.8871	9.9859	1.4839	7.8082	0.284	10.8286	-0.0196	-0.6446	0.621	-0.1212	-0.032	0.7241	-0.0232	-0.7686	0.0516	0.1596	0.1385	0.0109	0.1114	-0.0025	0.1699	17.6269	51.4637	35.7054
13	12.1999	-12.0581	2.3921	24.7394	-9.7096	4.6771	0.489	0.0019	-0.2538	-0.5785	0.1383	-0.1632	-0.0508	-0.2437	-0.6273	0.1791	-0.0448	0.0975	-0.0422	0.0224	0.1563	32.0577	51.9098	38.6868
14	27.4934	0.2904	2.5235	27.9044	5.5615	6.0353	-0.0992	-0.6492	0.9949	0.6147	-0.072	-0.7421	0.3682	1.0276	0.1712	0.0926	0.0121	0.0547	0.1097	0.0282	0.1523	38.6904	42.93	39.5692
15	3.2214	5.3902	-5.4879	9.0217	-9.2836	13.5469	0.1688	0.391	-0.1793	-0.2702	-0.181	0.118	0.1146	0.1746	0.0122	0.1785	0.0434	0.0779	0.0864	-0.0177	0.1618	36.7835	50.8141	22.6159
16	0.0454	0.3652	-0.0746	3.3442	0.1518	1.5174	0.0029	0.1257	0.0381	-0.5553	0.0173	-0.1441	0.4415	0.1524	-0.0201	0.1491	0.0126	0.0352	0.0151	-0.0152	0.1573	31.8111	35.6084	34.92
17	6.2092	5.9024	-2.6901	6.9228	-3.784	12.9325	0.0701	0.2764	-0.7823	0.1917	-0.0697	0.0175	0.204	-0.6616	-0.0003	0.1431	-0.0649	-0.011	0.1097	-0.0358	0.119	20.7241	27.1383	53.4677
18	28.2091	-24.68	-3.8801	50.1212	-9.3267	49.7736	1.0683	-0.7718	-1.0108	0.5521	-1.7405	-1.9328	3.3078	-3.1847	0.6722	0.0991	-0.2118	-0.0494	0.7009	0.0692	0.3417	11.1701	21.3921	65.7715

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 10
2	X-RAY DIFFRACTION	2	A	11 - 34
3	X-RAY DIFFRACTION	3	A	35 - 51
4	X-RAY DIFFRACTION	4	A	52 - 60
5	X-RAY DIFFRACTION	5	A	61 - 70
6	X-RAY DIFFRACTION	6	A	74 - 81
7	X-RAY DIFFRACTION	7	A	82 - 96
8	X-RAY DIFFRACTION	8	A	97 - 108
9	X-RAY DIFFRACTION	9	A	109 - 116
10	X-RAY DIFFRACTION	10	B	6 - 10
11	X-RAY DIFFRACTION	11	B	11 - 34
12	X-RAY DIFFRACTION	12	B	35 - 47
13	X-RAY DIFFRACTION	13	B	48 - 55
14	X-RAY DIFFRACTION	14	B	56 - 63
15	X-RAY DIFFRACTION	15	B	64 - 78
16	X-RAY DIFFRACTION	16	B	79 - 94
17	X-RAY DIFFRACTION	17	B	95 - 109
18	X-RAY DIFFRACTION	18	B	110 - 115

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