PDB-2xyo: Structural basis for a new tetracycline resistance mechanism rely...

ID or keywords:

Entry

Database: PDB / ID: 2xyo

Title

Structural basis for a new tetracycline resistance mechanism relying on the TetX monooxygenase

Components

TETX2

Keywords

OXIDOREDUCTASE / ANTIBIOTIC RESISTANCE / MONOOXYGENASE / TIGECYCLINE / TETRACYCLINE DEGRADATION

Function / homology

Function and homology information

tetracycline 11a-monooxygenase / FAD binding / monooxygenase activity / response to antibiotic / cytoplasm
Similarity search - Function

Biological species

BACTEROIDES THETAIOTAOMICRON (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 3 Å

Authors

Volkers, G. / Palm, G.J. / Weiss, M.S. / Hinrichs, W.

Citation

Journal: FEBS Lett. / Year: 2011
Title: Structural Basis for a New Tetracycline Resistance Mechanism Relying on the Tetx Monooxygenase.
Authors: Volkers, G. / Palm, G.J. / Weiss, M.S. / Wright, G.D. / Hinrichs, W.

History

Deposition	Nov 18, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 23, 2011	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Mar 6, 2019	Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4	Jul 17, 2019	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2xyo.cif.gz	585.3 KB	Display	PDBx/mmCIF format
PDB format	pdb2xyo.ent.gz	503.1 KB	Display	PDB format
PDBx/mmJSON format	2xyo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2xyo_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	2xyo_full_validation.pdf.gz	1.4 MB	Display
Data in XML	2xyo_validation.xml.gz	56.7 KB	Display
Data in CIF	2xyo_validation.cif.gz	73.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xy/2xyo ftp://data.pdbj.org/pub/pdb/validation_reports/xy/2xyo	HTTPS FTP

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Related structure data

Related structure data	2xdoC 2y6qC 2y6rC C: citing same article (ref.)
Similar structure data	4guv-3 3p9u-3 2xdo-3 3v3n-3 4a99-2 3v3n-1 2y6q-3 2y6r-3 2y6r-1 6ju1-d 3v3o-4 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

2xdoC

2y6qC

2y6rC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: TETX2

B: TETX2

C: TETX2

D: TETX2

hetero molecules

185 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: TETX2

hetero molecules

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

2

B: TETX2

hetero molecules

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

3

C: TETX2

hetero molecules

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

4

D: TETX2

hetero molecules

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

Unit cell

Length a, b, c (Å)	87.345, 68.658, 152.483
Angle α, β, γ (deg.)	90.00, 101.08, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	3	A	15 - 383
2	1	1	3	B	15 - 383
4	1	1	3	D	15 - 383
3	1	1	3	C	15 - 383

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.92085, -0.01904, 0.38944), (0.02219, -0.99975, 0.00358), (0.38928, 0.01194, 0.92104)	1.45742, 27.51358, -63.91325
2	given	(0.92002, 0.02744, -0.3909), (0.02562, -0.99962, -0.00988), (-0.39102, -0.00092, -0.92038)	27.45115, 57.9208, 138.40414
3	given	(0.91982, 0.02069, -0.3918), (0.01471, -0.99972, -0.01827), (-0.39207, 0.01104, -0.91987)	24.95196, 62.54359, 57.76976
4	given	(0.99994, -0.01087, -0.00125), (0.01088, 0.99991, 0.00835), (0.00116, -0.00837, 0.99996)	29.34893, -4.61539, 75.14562
5	given	(-0.92056, -0.01227, 0.39042), (0.0113, -0.99992, -0.0048), (0.39045, -1.0E-5, 0.92063)	3.78406, 33.04819, 16.66887
6	given	(-0.99996, -0.00841, 0.00171), (-0.00842, 0.9999, -0.01108), (-0.00161, -0.0111, -0.99994)	29.16241, -28.63923, 75.16801

#1: Protein	TETX2 Mass: 45353.207 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / Variant (production host): PRARE2 / References: UniProt: Q93L51
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.49 Å³/Da / Density % sol: 50.64 % Description: DATA WERE COLLECTED IN A MULTIPLE-WAVELENGTH ANOMALOUS-DISPERSION EXPERIMENT AT PEAK WAVELENGTH, INFLECTION AND HIGH ENERGY REMOTE. DATA STATISTICS ARE GIVEN FOR THE DATA COLLECTED AT ...Description: DATA WERE COLLECTED IN A MULTIPLE-WAVELENGTH ANOMALOUS-DISPERSION EXPERIMENT AT PEAK WAVELENGTH, INFLECTION AND HIGH ENERGY REMOTE. DATA STATISTICS ARE GIVEN FOR THE DATA COLLECTED AT PEAK WAVELENGTH, WHICH WERE ALSO USED FOR MODEL REFINEMENT.
Crystal grow	Temperature: 293 K / pH: 7 Details: 1.4 M AMMONIUM SULFATE, 100 MM SODIUM CITRATE BUFFER PH 7 AT 293 K

Crystal

Density Matthews: 2.49 Å³/Da / Density % sol: 50.64 %
Description: DATA WERE COLLECTED IN A MULTIPLE-WAVELENGTH ANOMALOUS-DISPERSION EXPERIMENT AT PEAK WAVELENGTH, INFLECTION AND HIGH ENERGY REMOTE. DATA STATISTICS ARE GIVEN FOR THE DATA COLLECTED AT ...

Crystal grow

Temperature: 293 K / pH: 7
Details: 1.4 M AMMONIUM SULFATE, 100 MM SODIUM CITRATE BUFFER PH 7 AT 293 K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

EMBL/DESY, HAMBURG

/ Beamline: X12 / Wavelength: 0.97784, 0.97838, 0.95369

Detector

Type: MARRESEARCH / Detector: CCD / Date: Feb 27, 2009

Radiation

Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97784	1
2	0.97838	1
3	0.95369	1

Reflection

Resolution: 3→99 Å / Num. obs: 35742 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / B_iso Wilson estimate: 53.8 Å² / R_merge(I) obs: 0.22 / Net I/σ(I): 11.7

Reflection shell

Resolution: 3→3.19 Å / Redundancy: 6.5 % / R_merge(I) obs: 0.73 / Mean I/σ(I) obs: 2.9 / % possible all: 98.8

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
Auto-Rickshaw		phasing
SHARP		phasing
REFMAC	5.5.0102	refinement

Refinement

Method to determine structure:

MAD
Starting model: NONE

Resolution: 3→149.64 Å / Cor.coef. F_o:F_c: 0.92 / Cor.coef. F_o:F_c free: 0.894 / SU B: 47.493 / SU ML: 0.421 / Cross valid method: THROUGHOUT / ESU R Free: 0.53 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. B VALUES WITH TLS ADDED. RESIDUES 247-249 ARE DISORDERED.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.29454	1783	5 %	RANDOM
R_work	0.24905	-	-	-
obs	0.25132	33933	99.42 %	-

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: 39.471 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.3 Å²	0 Å²	0.76 Å²
2-	-	1.03 Å²	0 Å²
3-	-	-	0.56 Å²

Refinement step

Cycle: LAST / Resolution: 3→149.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11421	0	258	0	11679

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	12000
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.519	1.978	16317
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.607	5	1478
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.697	25.442	588
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.19	15	1981
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.388	15	58
X-RAY DIFFRACTION	r_chiral_restr	0.101	0.2	1775
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	9186
X-RAY DIFFRACTION	r_gen_planes_other
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	0.415	1.5	7307
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.831	2	11758
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.465	3	4693
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.381	4.5	4549
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	1464	tight positional	0.04	0.05
2	B	1464	tight positional	0.04	0.05
3	C	1464	tight positional	0.04	0.05
4	D	1464	tight positional	0.04	0.05
1	A	1390	loose positional	0.05	5
2	B	1390	loose positional	0.05	5
3	C	1390	loose positional	0.04	5
4	D	1390	loose positional	0.04	5
1	A	1464	tight thermal	0.07	0.5
2	B	1464	tight thermal	0.07	0.5
3	C	1464	tight thermal	0.06	0.5
4	D	1464	tight thermal	0.06	0.5
1	A	1390	loose thermal	0.08	10
2	B	1390	loose thermal	0.08	10
3	C	1390	loose thermal	0.08	10
4	D	1390	loose thermal	0.07	10

LS refinement shell

Resolution: 3→3.078 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.391	139	-
R_work	0.329	2425	-
obs	-	-	98.5 %

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	2.3294	0.8288	-0.551	3.1025	-0.7209	2.9498	-0.0033	0.1469	0.4616	-0.0964	0.1412	0.314	-0.4836	-0.1248	-0.138	0.1278	0.036	0.0101	0.0349	0.0475	0.1121	18.8716	14.9236	16.2262
2	2.6049	0.9912	-0.1701	2.356	-0.5774	2.5719	0.0205	-0.1086	0.0722	0.0906	0.0771	0.0377	0.0197	0.0439	-0.0975	0.081	0.0285	0.0209	0.0916	-0.0648	0.0734	24.4236	3.2924	19.3342
3	2.438	0.8091	0.026	1.6004	-0.394	2.8041	-0.0253	-0.2824	-0.0574	0.1244	0.1726	-0.1943	0.1367	0.1235	-0.1473	0.0371	0.0562	-0.0025	0.1164	-0.0134	0.1034	26.1481	2.2051	26.027
4	3.1478	-2.1493	0.7671	18.8354	-3.2072	6.5367	0.1036	-0.6724	0.436	0.8336	0.6658	1.597	-0.4749	-0.2498	-0.7694	0.1182	-0.0053	0.1346	0.2816	-0.123	0.3525	23.3478	15.198	33.8496
5	1.6582	-0.7898	-0.2867	2.9497	0.43	2.3418	-0.0587	-0.0394	0.364	0.1151	0.058	-0.3066	-0.2961	-0.0031	0.0007	0.1196	-0.029	0.0068	0.0503	-0.0394	0.1111	10.0475	44.2882	58.454
6	2.6746	-1.1322	0.1385	2.4908	0.4772	2.1224	0.0148	0.1283	0.0463	-0.1147	0.0747	-0.0494	0.0079	0.0255	-0.0894	0.1103	-0.0477	0.0218	0.0873	0.0472	0.0626	4.5769	32.5932	55.4686
7	1.0804	-0.3219	0.1316	3.3982	0.0718	2.5271	-0.0059	0.2154	-0.1508	-0.0796	0.0096	0.1646	0.0981	-0.0421	-0.0038	0.0141	-0.0305	0.0054	0.1353	-0.0088	0.1633	2.8497	31.4196	48.7801
8	5.0186	-1.6452	-0.2635	23.7386	7.5858	9.1126	-0.1352	0.6605	0.2146	-0.9489	0.6856	-1.0098	-0.1507	0.383	-0.5504	0.14	-0.0005	0.0868	0.2786	0.1264	0.1827	5.5538	44.374	40.8272
9	3.4778	1.7338	0.4199	3.9384	-0.0461	2.5332	-0.0621	-0.258	-0.5204	-0.161	-0.1635	-0.5377	0.5005	0.3935	0.2257	0.1561	0.1406	0.057	0.2996	0.1559	0.1852	14.8785	12.6039	80.4977
10	2.3345	1.2945	-0.726	4.152	-0.4295	2.5706	0.0578	-0.5483	-0.0832	0.244	-0.1691	-0.1657	-0.0936	0.3169	0.1113	0.0743	0.0273	-0.0616	0.387	0.1045	0.1145	10.7343	24.1589	85.5175
11	1.3714	0.8565	-0.5612	4.6994	-0.2566	2.2634	0.093	-0.778	0.0401	0.4046	-0.2024	-0.0955	-0.2497	0.4366	0.1094	0.1544	-0.054	-0.111	0.5235	0.0341	0.2446	11.7449	25.2618	92.3655
12	1.9716	1.57	-0.3229	12.9372	-0.092	4.9055	0.0301	-0.787	-0.6332	1.183	0.1923	-1.5228	0.2788	0.777	-0.2224	0.1919	0.0611	-0.1364	0.7413	0.2556	0.5258	17.6516	12.39	98.4867
13	2.3605	1.2236	-0.1428	3.554	0.2783	2.6552	-0.0798	-0.2973	-0.456	-0.1057	-0.208	-0.4704	0.5252	0.6249	0.2878	0.1743	0.1508	0.0235	0.3425	0.1548	0.1972	-14.233	17.3929	5.5641
14	2.3329	1.1032	-0.8816	3.9322	-0.4471	2.9744	0.0045	-0.5996	-0.0467	0.2892	-0.1268	-0.1694	-0.0702	0.5016	0.1223	0.0888	0.0336	-0.0764	0.4419	0.0643	0.0953	-18.2865	28.9463	10.6426
15	1.1022	0.6115	-0.8464	5.0953	-0.6064	2.6004	0.1348	-0.7878	0.0365	0.4747	-0.2675	0.0675	-0.2745	0.5991	0.1327	0.2017	-0.0583	-0.0916	0.6052	0.0317	0.225	-17.2641	30.0132	17.5023
16	2.842	3.9103	-1.5224	17.4418	0.7689	5.6801	-0.0701	-0.8811	-0.4067	1.4123	0.3294	-1.041	0.3126	1.0054	-0.2593	0.2429	0.1167	-0.1842	0.8657	0.2628	0.4948	-11.4492	17.0563	23.558

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	15 - 93
2	X-RAY DIFFRACTION	2	A	94 - 259
3	X-RAY DIFFRACTION	3	A	260 - 334
4	X-RAY DIFFRACTION	4	A	335 - 383
5	X-RAY DIFFRACTION	5	B	15 - 93
6	X-RAY DIFFRACTION	6	B	94 - 259
7	X-RAY DIFFRACTION	7	B	260 - 334
8	X-RAY DIFFRACTION	8	B	335 - 383
9	X-RAY DIFFRACTION	9	D	15 - 93
10	X-RAY DIFFRACTION	10	D	94 - 259
11	X-RAY DIFFRACTION	11	D	260 - 334
12	X-RAY DIFFRACTION	12	D	335 - 383
13	X-RAY DIFFRACTION	13	C	15 - 93
14	X-RAY DIFFRACTION	14	C	94 - 259
15	X-RAY DIFFRACTION	15	C	260 - 334
16	X-RAY DIFFRACTION	16	C	335 - 383

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