PDB-3ech: The MarR-family repressor MexR in complex with its antirepressor ArmR

ID or keywords:

Entry

Database: PDB / ID: 3ech

Title

The MarR-family repressor MexR in complex with its antirepressor ArmR

Components

25-mer fragment of protein ArmR
Multidrug resistance operon repressor

Keywords

Transcription / Transcription regulation / winged helix / helix-turn-helix / protein-peptide complex / DNA-binding / Repressor

Function / homology

Function and homology information

negative regulation of transmembrane transport / positive regulation of transporter activity / DNA-binding transcription repressor activity / negative regulation of protein secretion / protein-DNA complex / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / identical protein binding
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.802 Å

Authors

Wilke, M.S. / Strynadka, N.C.J.

Citation

Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: The crystal structure of MexR from Pseudomonas aeruginosa in complex with its antirepressor ArmR
Authors: Wilke, M.S. / Heller, M. / Creagh, A.L. / Haynes, C.A. / McIntosh, L.P. / Poole, K. / Strynadka, N.C.J.

History

Deposition	Aug 30, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 21, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.name / _software.version
Revision 1.3	Oct 20, 2021	Group: Database references / Category: database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4	Aug 30, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3ech.cif.gz	78.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3ech.ent.gz	59.9 KB	Display	PDB format
PDBx/mmJSON format	3ech.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3ech_validation.pdf.gz	442.5 KB	Display	wwPDB validaton report
Full document	3ech_full_validation.pdf.gz	446.6 KB	Display
Data in XML	3ech_validation.xml.gz	15.4 KB	Display
Data in CIF	3ech_validation.cif.gz	21.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ec/3ech ftp://data.pdbj.org/pub/pdb/validation_reports/ec/3ech	HTTPS FTP

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Related structure data

Related structure data	1lnwS S: Starting model for refinement
Similar structure data	6fp6-8 6fp6-3 6fp6-1 6fp6-7 4dfb-1 2fh1-3 2fh4-3 4rma-2 2ply-1 6fp6-5 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

Deposited unit

A: Multidrug resistance operon repressor

B: Multidrug resistance operon repressor

C: 25-mer fragment of protein ArmR

36.1 kDa, 3 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)	52.201, 57.151, 91.931
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Multidrug resistance operon repressor / MexR Mass: 16447.025 Da / Num. of mol.: 2 / Fragment: residues 1-142 / Mutation: Q106L, A110L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: mexR, PA0424 / Plasmid: pET41a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P52003
#2: Protein/peptide	25-mer fragment of protein ArmR Mass: 3250.569 Da / Num. of mol.: 1 / Fragment: residues 29-53 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA3719 / Plasmid: pTYB12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9HXS2
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 212 / 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: 1.9 Å³/Da / Density % sol: 35.16 %
Crystal grow	Temperature: 291 K / Method: microbatch / pH: 5.5 Details: 20% PEG 3000, 0.1M sodium citrate, pH 5.5, microbatch, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Details: KOHZU: Double Crystal Si(111)
Radiation	Monochromator: KOHZU: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.802→48.56 Å / Num. obs: 26074 / Redundancy: 7.9 % / R_sym value: 0.061 / Net I/σ(I): 35.1
Reflection shell	Resolution: 1.802→1.86 Å / Redundancy: 8 % / Mean I/σ(I) obs: 3 / R_sym value: 0.056

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
MOLREP		phasing
REFMAC	5.2	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1LNW

1lnw

Resolution: 1.802→48.56 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.924 / SU B: 5.023 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2291	1325	5.1 %	RANDOM
R_work	0.17558	-	-	-
all	0.1782	24697	-	-
obs	0.1782	24697	99.82 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 12.527 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.81 Å²	0 Å²	0 Å²
2-	-	-0.04 Å²	0 Å²
3-	-	-	-0.77 Å²

Refinement step

Cycle: LAST / Resolution: 1.802→48.56 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2346	0	0	212	2558

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.021	2502
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1737
X-RAY DIFFRACTION	r_angle_refined_deg	1.401	1.98	3411
X-RAY DIFFRACTION	r_angle_other_deg	0.966	3	4238
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.515	5	315
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.269	23.358	134
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.71	15	471
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.283	15	30
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	396
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	2762
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	499
X-RAY DIFFRACTION	r_nbd_refined	0.237	0.2	592
X-RAY DIFFRACTION	r_nbd_other	0.189	0.2	1780
X-RAY DIFFRACTION	r_nbtor_refined	0.173	0.2	1216
X-RAY DIFFRACTION	r_nbtor_other	0.083	0.2	1313
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.174	0.2	167
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	0.234	0.2	36
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.246	0.2	85
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.185	0.2	28
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	1.032	1.5	1993
X-RAY DIFFRACTION	r_mcbond_other	0.244	1.5	584
X-RAY DIFFRACTION	r_mcangle_it	1.162	2	2444
X-RAY DIFFRACTION	r_scbond_it	2.259	3	1084
X-RAY DIFFRACTION	r_scangle_it	3.357	4.5	950
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.802→1.849 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.236	96	-
R_work	0.181	1759	-
obs	-	-	97.68 %

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	12.7218	2.861	4.6245	6.6687	1.2087	6.8811	0.0535	0.2746	-0.1805	0.2124	0.0978	-0.5016	0.1938	0.7975	-0.1513	0.0998	0.025	-0.0512	0.0794	-0.0071	0.0399	9.1694	-4.8075	1.2898
2	14.769	-2.7148	5.192	1.8761	-1.3326	3.4992	0.175	-0.3524	-0.0356	0.0444	0.0526	0.2453	0.1785	-0.3561	-0.2275	0.0919	-0.0292	0.0109	0.0548	0.016	0.0401	-14.4651	-1.0087	-4.437
3	3.2427	1.0308	-2.321	3.2564	-2.7816	6.4678	-0.0898	0.1994	-0.1004	-0.1572	0.0415	0.0015	0.1824	-0.2078	0.0483	0.1157	-0.0291	-0.0018	0.1143	-0.0318	0.1334	-15.8435	7.1256	-23.2954
4	44.8332	-18.2467	-9.9	27.7015	10.9031	13.9902	0.1882	1.493	-3.0029	-0.4741	-0.3444	-0.4582	1.123	0.2226	0.1562	0.1114	-0.1291	0.0442	0.067	-0.2053	0.2123	-20.8713	-0.0206	-28.0431
5	12.688	3.6499	-2.7931	4.539	-2.6654	5.5552	-0.2945	0.9796	0.1667	-0.4452	0.3262	0.0766	0.0707	-0.539	-0.0317	0.0831	-0.0534	-0.0241	0.1976	-0.0095	0.0131	-24.7893	11.1903	-26.6476
6	5.2072	-0.6155	4.6285	2.1355	-1.0393	8.0067	-0.1335	-0.0505	0.1341	0.1045	0.0574	-0.0877	-0.2153	-0.1347	0.0761	0.0424	0.0222	-0.0028	0.0477	-0.024	0.0447	-20.2705	11.6515	-11.6093
7	3.0008	0.4372	0.7026	1.9702	0.5547	2.855	0.0987	-0.2209	0.024	0.0568	-0.0331	0.0341	-0.0878	-0.1416	-0.0656	0.0967	-0.0109	-0.0081	0.0433	-0.0128	0.0274	-5.1484	9.2296	3.1129
8	24.7635	3.8782	-21.9346	33.6587	3.7447	25.6937	0.1439	-0.3095	0.0059	-0.0957	-0.1222	-0.7378	-0.0894	0.6127	-0.0217	0.1044	0.0086	-0.0415	0.0888	-0.0451	0.0996	9.6398	6.0726	-6.3656
9	54.1331	-0.317	-35.6182	1.1476	-0.1775	23.5659	0.1765	-0.9398	0.7341	0.0727	0.3971	0.0137	-0.0548	0.3901	-0.5736	0.1645	0.0193	0.0146	0.0398	-0.04	0.0378	-12.1881	15.9085	7.2094
10	0.9093	-1.5932	-1.8165	4.6327	3.4578	4.1665	0.0551	0.0232	-0.0192	-0.078	-0.0551	-0.0469	-0.1182	0.022	0	0.0601	0.0072	-0.0044	0.0428	-0.0098	0.0509	0.3104	2.2243	-11.7265
11	6.7705	3.7514	-2.6132	5.909	-2.0719	2.6158	-0.0769	-0.1618	0.0103	0.1189	0.0732	0.1019	0.0341	-0.1493	0.0037	0.1089	0.0075	0.0211	0.0809	-0.0283	0.0645	-8.7756	-17.3174	-15.9813
12	11.9918	-3.8753	-2.91	6.4433	0.7026	8.0281	0.0101	0.0684	0.4515	-0.0676	0.1673	0.1604	-0.5114	-0.5083	-0.1774	0.1104	0.01	0.0022	0.0515	0.0196	0.063	-10.2821	-17.7968	-25.5135
13	12.4876	6.7527	-4.2107	7.5083	-0.8152	4.356	-0.203	0.3104	-0.1776	0.1622	0.0952	0.5956	0.4018	-0.4723	0.1078	0.0919	-0.0271	0.0406	0.0363	-0.0104	0.1208	-12.7444	-29.8253	-21.02
14	9.5649	3.2833	1.7533	4.6055	2.1395	3.5666	-0.0044	0.1675	-0.4961	0.0679	-0.0075	0.1038	0.1512	-0.2157	0.0119	0.103	-0.0066	0.0346	0.0272	0.026	0.0922	-7.8261	-26.0664	-18.6342
15	0.2398	1.1574	0.3926	8.4266	5.8514	6.1554	-0.0569	-0.0399	-0.0943	0.026	0.0738	-0.1453	0.0411	0.121	-0.0169	0.0743	0.0144	-0.0294	0.0538	-0.0055	0.0657	7.0718	-6.9526	-7.9673
16	16.5875	0.6157	0.9486	4.2595	0.5607	2.5537	0.0009	-0.7945	-0.1298	0.1608	0.0435	0.2013	0.035	-0.1744	-0.0444	0.1069	-0.0108	-0.0452	0.0548	0.0112	0.0157	1.2492	1.0957	7.024
17	19.3339	-0.4376	2.6604	1.8977	-1.4601	7.7656	-0.0879	0.7787	1.243	0.314	0.1438	0.1009	-0.9277	0.4253	-0.0559	0.1375	-0.0299	0.0241	0.0183	0.0227	0.07	3.5219	14.571	-12.5011
18	28.7448	4.4523	5.6811	14.9008	11.2657	8.7129	0.0995	0.8007	1.0523	0.2436	-0.1102	0.8904	0.0247	0.1146	0.0107	0.0426	0.0226	0.0347	0.0157	0.0843	0.1327	-6.1302	9.9728	-14.7601
19	7.6879	-6.3688	0.6081	8.0966	-0.1568	0.6048	0.1405	0.2507	-0.1093	-0.0423	-0.181	-0.0402	0.0348	-0.1429	0.0406	0.0314	-0.0041	0.0043	0.0284	-0.0199	0.0333	-7.9737	-0.6581	-12.989

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 10
2	X-RAY DIFFRACTION	2	A	11 - 31
3	X-RAY DIFFRACTION	3	A	32 - 62
4	X-RAY DIFFRACTION	4	A	66 - 76
5	X-RAY DIFFRACTION	5	A	77 - 100
6	X-RAY DIFFRACTION	6	A	101 - 113
7	X-RAY DIFFRACTION	7	A	114 - 136
8	X-RAY DIFFRACTION	8	A	137 - 142
9	X-RAY DIFFRACTION	9	B	1 - 5
10	X-RAY DIFFRACTION	10	B	6 - 31
11	X-RAY DIFFRACTION	11	B	32 - 60
12	X-RAY DIFFRACTION	12	B	61 - 78
13	X-RAY DIFFRACTION	13	B	79 - 89
14	X-RAY DIFFRACTION	14	B	90 - 106
15	X-RAY DIFFRACTION	15	B	107 - 123
16	X-RAY DIFFRACTION	16	B	124 - 141
17	X-RAY DIFFRACTION	17	C	30 - 38
18	X-RAY DIFFRACTION	18	C	39 - 43
19	X-RAY DIFFRACTION	19	C	44 - 53

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