PDB-3vvp: Crystal structure of MATE in complex with Br-NRF

ID or keywords:

Entry

Database: PDB / ID: 3vvp

Title

Crystal structure of MATE in complex with Br-NRF

Components

Putative uncharacterized protein

Keywords

TRANSPORT PROTEIN / MATE / multidrug transporter / ligand-bound

Function / homology

: / Multi antimicrobial extrusion protein / MatE / antiporter activity / xenobiotic transmembrane transporter activity / plasma membrane / Chem-BNU / MATE family efflux transporter

Function and homology information

Biological species

Pyrococcus furiosus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.91 Å

Authors

Tanaka, Y. / Ishitani, R. / Nureki, O.

Citation

Journal: Nature / Year: 2013
Title: Structural basis for the drug extrusion mechanism by a MATE multidrug transporter.
Authors: Tanaka, Y. / Hipolito, C.J. / Maturana, A.D. / Ito, K. / Kuroda, T. / Higuchi, T. / Katoh, T. / Kato, H.E. / Hattori, M. / Kumazaki, K. / Tsukazaki, T. / Ishitani, R. / Suga, H. / Nureki, O.

History

Deposition	Jul 27, 2012	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 3, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jan 29, 2014	Group: Database references
Revision 1.2	Nov 22, 2017	Group: Refinement description / Category: software
Revision 1.3	Nov 8, 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_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	3vvp.cif.gz	299.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3vvp.ent.gz	245.9 KB	Display	PDB format
PDBx/mmJSON format	3vvp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3vvp_validation.pdf.gz	714.5 KB	Display	wwPDB validaton report
Full document	3vvp_full_validation.pdf.gz	719.9 KB	Display
Data in XML	3vvp_validation.xml.gz	17.2 KB	Display
Data in CIF	3vvp_validation.cif.gz	25.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vv/3vvp ftp://data.pdbj.org/pub/pdb/validation_reports/vv/3vvp	HTTPS FTP

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Related structure data

Related structure data	3vvnSC 3vvoC 3vvrC 3vvsC 3w4tC 3wbnC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3tgq-1 2zba-3 5hiw-d 3o69-d 4x94-d 2yvm-1 3cy1-d 3e5j-d 3rwl-d 3vsd-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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: Putative uncharacterized protein

B: Putative uncharacterized protein

hetero molecules

98.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative uncharacterized protein

hetero molecules

defined by author
49.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Putative uncharacterized protein

defined by author
49.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	122.368, 122.368, 110.384
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	168
Space group name H-M	P6

#1: Protein	Putative uncharacterized protein / Archaeal-type transporter Mass: 49276.258 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: JCM 8422 / Gene: PF0708 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q8U2X0
#2: Chemical	ChemComp-BNU / 6-bromo-1-ethyl-4-oxo-7-(piperazin-1-yl)-1,4-dihydroquinoline-3-carboxylic acid Mass: 380.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₆H₁₈BrN₃O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.42 Å³/Da / Density % sol: 49.19 % / Mosaicity: 0.608 °
Crystal grow	Temperature: 293 K / Method: lipdic cubic phase / pH: 8 Details: 28% PEG 550MME, 100mM Tris-HCl, 100mM Li2SO4, pH 8.0, lipdic cubic phase, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SPring-8

/ Beamline: BL32XU / Wavelength: 0.91 Å

Detector

Type: RAYONIX MX225HE / Detector: CCD / Date: May 16, 2012

Radiation

Monochromator: liquid nitrogen cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.91 Å / Relative weight: 1

Reflection

Resolution: 2.9→50 Å / Num. all: 20596 / Num. obs: 20596 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.1 % / R_merge(I) obs: 0.291 / Χ²: 2.533 / Net I/σ(I): 3.9

Reflection shell

Resolution (Å)	Redundancy (%)	Num. unique all	Χ²	Diffraction-ID	% possible all	R_merge(I) obs
2.9-2.95	20.7	988	1.913	1	100
2.95-3	21.1	1040	1.945	1	100
3-3.06	21.2	1027	1.954	1	100
3.06-3.12	21.2	1024	1.975	1	100
3.12-3.19	21.3	1018	2.033	1	100
3.19-3.27	21.5	1042	2.085	1	100
3.27-3.35	21.4	1033	2.134	1	100
3.35-3.44	21.5	1008	2.189	1	100	0.965
3.44-3.54	21.5	1027	2.239	1	100	0.912
3.54-3.65	21.6	1035	2.352	1	99.9	0.741
3.65-3.78	21.6	1032	2.562	1	100	0.56
3.78-3.94	21.6	1030	2.653	1	100	0.496
3.94-4.11	21.6	1018	2.836	1	100	0.379
4.11-4.33	21.5	1032	3.07	1	99.9	0.305
4.33-4.6	15	1019	3.684	1	99.8	0.239
4.6-4.96	21.7	1045	3.18	1	100	0.237
4.96-5.46	21.8	1032	2.823	1	100	0.261
5.46-6.24	21.7	1033	2.639	1	100	0.29
6.24-7.86	21.3	1053	3.116	1	100	0.166
7.86-50	20.3	1060	3.549	1	99.3	0.085

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHENIX	1.8_1069	refinement
PDB_EXTRACT	3.11	data extraction
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3VVN

3vvn

Resolution: 2.91→48.951 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7121 / SU ML: 0.53 / σ(F): 1.37 / Phase error: 35.39 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.3264	1987	9.65 %	RANDOM
R_work	0.2848	-	-	-
all	0.2888	20588	-	-
obs	0.2888	20588	99.48 %	-

Solvent computation

Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 468.64 Å² / B_iso mean: 51.6823 Å² / B_iso min: 0 Å²

Refinement step

Cycle: LAST / Resolution: 2.91→48.951 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5752	0	23	14	5789

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	5874
X-RAY DIFFRACTION	f_angle_d	0.697	8025
X-RAY DIFFRACTION	f_chiral_restr	0.04	1010
X-RAY DIFFRACTION	f_plane_restr	0.004	997
X-RAY DIFFRACTION	f_dihedral_angle_d	12.268	1871

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.9105-2.9832	0.3893	131	0.321	1266	1397	94
2.9832-3.0639	0.4005	141	0.3017	1328	1469	100
3.0639-3.154	0.3337	138	0.3179	1324	1462	100
3.154-3.2558	0.3564	141	0.3092	1301	1442	100
3.2558-3.3721	0.3512	146	0.3063	1342	1488	100
3.3721-3.5071	0.3278	147	0.2858	1330	1477	100
3.5071-3.6667	0.3493	141	0.2872	1322	1463	100
3.6667-3.8599	0.326	146	0.2715	1327	1473	100
3.8599-4.1016	0.345	141	0.2709	1335	1476	100
4.1016-4.4181	0.3057	142	0.2563	1340	1482	100
4.4181-4.8624	0.3097	140	0.2852	1334	1474	100
4.8624-5.5652	0.3541	145	0.2913	1347	1492	100
5.5652-7.0082	0.3168	142	0.3086	1339	1481	100
7.0082-48.958	0.2856	146	0.2709	1366	1512	99

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	1.28	-0.2235	1.0832	0.3691	-0.1527	0.6027	0.0993	-0.1059	-0.0212	0.0918	-0.0462	0.0597	0.0561	0.0073	-0.0127	0.2476	0.008	0.0346	0.2781	-0.0555	0.3083	-117.0462	51.5566	3.9761
2	0.8823	0.0952	0.06	1.1459	-0.2966	0.2356	0.1588	-0.2513	-0.0911	-0.0928	0.0489	0.2682	0.2564	0.5457	-0.0068	0.253	0.1083	-0.0376	0.5086	-0.0507	0.3719	-127.3768	52.2252	4.113
3	0.2132	-0.0201	-0.0662	1.1178	1.2502	1.3519	0.1324	-0.1562	-0.1427	0.1225	-0.1367	-0.4258	-0.1395	-0.0175	-0.0784	0.3847	0.0469	-0.2895	0.2402	0.5281	0.7599	-104.6372	48.3112	-1.208
4	0.8876	-0.6157	-0.2283	0.338	-0.1591	1.5285	-0.1422	-0.1038	-0.0357	0.0073	0.1066	0.0316	0.3879	0.028	0.022	0.3325	0.0286	-0.0433	0.2901	0.0056	0.32	-106.1874	34.2266	1.2286
5	1.0568	-0.3189	0.722	0.8174	0.0222	1.7664	-0.5022	0.239	0.1845	-0.0617	-0.2409	0.4311	-0.579	0.0963	-0.3194	0.5893	0.4004	-0.3189	0.5981	-0.0669	0.211	-97.4312	33.2306	4.026
6	0.6306	0.4637	0.1814	0.3308	0.2459	0.2001	0.0531	0.1323	-0.0353	0.1159	0.179	0.1849	-0.4596	0.5435	-0.0225	0.4745	-0.0152	0.0249	0.364	0.0027	0.3021	-131.7958	44.1433	55.1999
7	2.556	-0.2197	0.1715	1.5385	-0.7276	1.8941	-0.0606	0.6233	-0.0965	-0.1459	0.3595	0.0846	0.1526	-0.7112	0.0262	0.4065	-0.0608	0.0284	0.4162	-0.0607	0.6356	-136.5059	59.1996	46.7171
8	0.3002	-0.1429	0.2613	0.4072	0.4548	1.2319	-0.0459	-0.4376	0.7989	-0.0534	0.2557	0.0394	-0.1429	0.0294	0.2715	0.1135	-0.0762	-0.1929	0.6597	-0.3471	0.8627	-132.0136	57.5946	62.8404
9	0.7729	-0.0573	0.0052	1.7132	0.6604	0.4639	-0.2361	0.198	-0.1362	0.2476	0.369	-0.7291	-0.1786	0.6162	0.0823	0.4491	-0.0061	0.1092	0.5224	0.0956	0.4646	-123.3569	52.3701	52.4704
10	0.9929	0.645	-1.3243	0.469	-0.2658	4.3033	-0.4265	-0.4452	-0.2179	0.0674	-0.4655	-0.0444	0.4521	-0.0337	-0.1768	0.1222	0.1468	-0.0237	0.6544	-0.0833	0.5335	-144.6812	46.2805	59.4681
11	0.7357	0.1096	-0.082	0.1871	-0.0381	0.0096	0.0826	-0.405	-0.6	0.1604	0.1484	0.0281	0.081	0.2868	0.1146	-0.0999	-0.3747	-0.1972	0.7085	-0.0665	0.5033	-137.0694	35.2879	57.1243
12	1.8672	0.4652	0.48	1.1048	-0.0521	3.1352	0.1806	0.2883	-0.459	0.1971	0.1228	0.0568	0.0855	-0.2474	-0.1298	0.4653	-0.0223	-0.0341	0.3528	0.0796	0.525	-138.1871	25.704	54.0411
13	1.5271	0.8258	-1.2115	0.8195	-0.3681	1.6414	-0.1508	0.1881	-0.191	-0.9699	-0.5716	-0.3546	-0.4345	0.786	0.0615	0.5983	0.0012	-0.1274	0.4644	0.1483	0.4816	-147.0366	38.2995	52.2522
14	1.5074	0.0682	0.2353	1.9016	0.3887	2.6702	0.4282	-0.5804	-0.0727	-0.0779	0.6878	0.4452	1.096	-0.6989	-0.0666	0.4361	0.0621	-0.0378	0.7061	0.1871	0.3977	-151.0622	30.0377	73.1107
15	2.8941	0.4064	-0.4778	1.2764	0.4589	0.3008	-0.2621	0.2029	0.0992	0.8191	0.2936	0.2119	-0.0662	0.324	0.148	0.7033	-0.0913	0.0204	0.3828	0.0967	0.2796	-149.0949	28.8511	58.9043

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ 4:165)	A	4 - 165
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 166:235)	A	166 - 235
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESSEQ 236:269)	A	236 - 269
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESSEQ 270:422)	A	270 - 422
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESSEQ 423:453)	A	423 - 453
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESSEQ 4:86)	B	4 - 86
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESSEQ 87:115)	B	87 - 115
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESSEQ 116:161)	B	116 - 161
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESSEQ 162:235)	B	162 - 235
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESSEQ 236:269)	B	236 - 269
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESSEQ 270:312)	B	270 - 312
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESSEQ 313:375)	B	313 - 375
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESSEQ 376:403)	B	376 - 403
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESSEQ 404:422)	B	404 - 422
15	X-RAY DIFFRACTION	15	CHAIN B AND (RESSEQ 423:447)	B	423 - 447

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