PDB-2xdo: Structure of the Tetracycline degrading Monooxygenase TetX2 from ...

ID or keywords:

Entry

Database: PDB / ID: 2xdo

Title

Structure of the Tetracycline degrading Monooxygenase TetX2 from Bacteroides thetaiotaomicron

Components

TETX2 PROTEIN

Keywords

OXIDOREDUCTASE / TETRACYCLINE DEGRADATION / TIGECYCLINE / FLAVIN / BACTEROIDES FRAGILI

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 /

MOLECULAR REPLACEMENT / Resolution: 2.09 Å

Authors

Volkers, G. / Palm, G.J. / Wright, G.D. / 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	May 5, 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	May 1, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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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PDBx/mmCIF format	2xdo.cif.gz	603.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2xdo.ent.gz	500.8 KB	Display	PDB format
PDBx/mmJSON format	2xdo.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xd/2xdo ftp://data.pdbj.org/pub/pdb/validation_reports/xd/2xdo	HTTPS FTP

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Related structure data

Related structure data	2xyoC 2y6qC 2y6rC C: citing same article (ref.)
Similar structure data	4guv-2 3v3o-2 4guv-1 3v3n-4 3v3o-1 4a99-3 2y6q-3 2y6r-2 4a6n-1 2y6q-4 2y6q-2 3v3o-3 4a99-2 4a6n-4 2xyo-3 3p9u-1 3v3n-1 2xyo-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) 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

2xyoC

2y6qC

2y6rC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: TETX2 PROTEIN

B: TETX2 PROTEIN

C: TETX2 PROTEIN

D: TETX2 PROTEIN

hetero molecules

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

1

A: TETX2 PROTEIN

hetero molecules

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

2

B: TETX2 PROTEIN

hetero molecules

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

3

C: TETX2 PROTEIN

hetero molecules

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

4

D: TETX2 PROTEIN

hetero molecules

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

Unit cell

Length a, b, c (Å)	68.110, 80.270, 86.890
Angle α, β, γ (deg.)	111.00, 90.23, 93.43
Int Tables number	1
Space group name H-M	P1

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
3	1	1	3	C	15 - 383
4	1	1	3	D	15 - 383

#1: Protein	TETX2 PROTEIN Mass: 44703.395 Da / Num. of mol.: 4 / Fragment: FAD-BINDING DOMAIN, RESIDUES 11-388 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / 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.: 13 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 571 / 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: 2.46 Å³/Da / Density % sol: 49.97 % / Description: NONE
Crystal grow	Details: 1.5 M AMMONIUM SULFATE, 0.1 M SODIUM CITRATE PH 7

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.918
Detector	Type: MARRESEARCH / Detector: CCD / Date: Nov 13, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.918 Å / Relative weight: 1
Reflection	Resolution: 2.09→49.06 Å / Num. obs: 91733 / % possible obs: 92.2 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / R_merge(I) obs: 0.06 / Net I/σ(I): 7.5
Reflection shell	Resolution: 2.09→2.2 Å / Redundancy: 2.1 % / R_merge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / % possible all: 64

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0110	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: SELENOMETHIONINE DERIVATIVE

Resolution: 2.09→40.54 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.933 / SU B: 10.029 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.235 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22993	4607	5 %	RANDOM
R_work	0.1899	-	-	-
obs	0.19192	87111	90.46 %	-

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: 39.78 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.83 Å²	-0.86 Å²	0.11 Å²
2-	-	-0.13 Å²	-0.37 Å²
3-	-	-	-1.06 Å²

Refinement step

Cycle: LAST / Resolution: 2.09→40.54 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11335	0	277	571	12183

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.023	0.022	11851
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.067	1.982	16119
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.065	5	1454
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.218	25.565	566
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.926	15	1927
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.696	15	51
X-RAY DIFFRACTION	r_chiral_restr	0.149	0.2	1765
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.021	9026
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	0.904	1.5	7258
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.655	2	11653
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.813	3	4593
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	4.438	4.5	4466
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	1432	tight positional	0.07	0.05
2	B	1432	tight positional	0.08	0.05
3	C	1432	tight positional	0.06	0.05
4	D	1432	tight positional	0.07	0.05
1	A	1338	loose positional	0.13	5
2	B	1338	loose positional	0.11	5
3	C	1338	loose positional	0.09	5
4	D	1338	loose positional	0.09	5
1	A	1432	tight thermal	0.26	0.5
2	B	1432	tight thermal	0.25	0.5
3	C	1432	tight thermal	0.22	0.5
4	D	1432	tight thermal	0.22	0.5
1	A	1338	loose thermal	0.28	10
2	B	1338	loose thermal	0.27	10
3	C	1338	loose thermal	0.23	10
4	D	1338	loose thermal	0.23	10

LS refinement shell

Resolution: 2.091→2.145 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.284	141	-
R_work	0.258	3056	-
obs	-	-	42.69 %

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	1.5306	0.3177	0.4256	1.7342	-0.1302	1.8128	0.0869	-0.1135	-0.031	0.0164	-0.005	0.3384	0.018	-0.3403	-0.0819	0.0689	-0.0357	0.0092	0.1411	0.0353	0.1295	-15.8467	-0.8688	14.9502
2	1.3735	0.2018	0.6982	1.2547	0.2465	1.7025	0.0919	0.0183	0.0806	-0.0932	-0.0103	0.2227	-0.0147	-0.2146	-0.0816	0.0839	-0.0022	0.0146	0.1194	0.022	0.0846	-11.0381	4.657	9.8319
3	2.273	0.4176	-0.103	2.523	0.2162	2.7166	0.0975	0.195	0.048	-0.1606	0.0744	-0.2993	-0.056	0.3569	-0.1718	0.0732	-0.03	0.0175	0.146	-0.0316	0.1119	13.6145	4.8482	15.1169
4	3.4636	-0.3755	-0.102	2.803	-0.2875	2.217	0.0922	-0.3122	0.3199	0.1884	0.0261	0.3055	-0.4136	-0.168	-0.1183	0.1696	0.0585	0.052	0.114	0.0092	0.1308	-13.6582	16.3194	14.7415
5	2.0701	0.3573	-0.5313	1.9031	0.1549	2.0528	0.0852	0.176	0.1286	-0.0048	-0.0879	0.2742	-0.1865	-0.3325	0.0026	0.0584	0.0349	-0.01	0.1514	0.008	0.0905	13.8356	36.4137	40.8444
6	1.549	-0.0056	-0.4784	1.6916	0.1073	1.5748	0.0544	0.0729	-0.0493	0.1128	-0.0231	0.1321	0.0407	-0.1677	-0.0313	0.0785	-0.0207	-0.0169	0.1273	-0.0076	0.0457	18.605	30.7309	46.0363
7	2.6655	0.1869	-0.5886	2.7669	0.1254	2.3431	0.1003	-0.2138	-0.184	0.1017	-0.0048	-0.5319	0.0494	0.45	-0.0955	0.0396	-0.0047	-0.0358	0.1912	-0.0217	0.2129	43.2576	30.4364	40.5855
8	2.8499	0.453	-0.7029	2.6468	0.337	2.0015	-0.0482	0.1656	-0.2534	0.0102	-0.0365	0.1469	0.3352	-0.2758	0.0846	0.1074	-0.0783	-0.0136	0.1304	-0.0282	0.0676	15.94	19.2164	40.8291
9	2.1636	0.1801	0.1865	1.9871	-0.1147	2.3286	0.0073	0.1626	0.0898	-0.1807	0.048	-0.373	-0.2019	0.4352	-0.0553	0.1936	-0.1033	0.0195	0.1962	0.0026	0.1569	-14.8768	-23.5562	44.1826
10	2.0611	0.1585	0.5089	1.659	0.1	2.0795	-0.0694	0.0543	0.1588	-0.0032	0.0596	-0.2001	-0.337	0.2889	0.0099	0.2423	-0.1026	-0.0183	0.1258	0.0268	0.1102	-19.5189	-20.083	51.1694
11	4.2027	-0.0593	-0.3186	2.8023	0.4936	2.5093	-0.1058	-0.1831	0.2621	0.0383	-0.0035	0.3754	-0.3245	-0.3839	0.1093	0.2745	0.0955	-0.0408	0.179	0.0398	0.2421	-44.2907	-17.9176	46.3949
12	4.5683	0.4822	0.7261	2.0818	0.3663	1.8109	-0.1143	0.1177	0.6082	-0.0381	0.019	-0.1164	-0.7074	0.2645	0.0953	0.4349	-0.1463	-0.0437	0.1406	0.0413	0.2204	-16.9498	-7.3433	49.9869
13	2.4686	-0.1404	-0.6961	1.9227	0.2452	2.2444	-0.1034	-0.3289	-0.1837	0.2768	0.1186	-0.3157	0.3682	0.5383	-0.0152	0.2749	0.132	-0.0462	0.2351	-0.0175	0.1419	19.6207	-22.1268	11.5224
14	2.3499	-0.0757	-0.7966	1.6215	0.1749	1.9218	-0.1506	-0.1261	-0.2106	0.106	0.0984	-0.2138	0.4715	0.3255	0.0522	0.3025	0.1069	0.0076	0.1339	-0.0004	0.116	14.9725	-25.5918	4.3266
15	4.0134	0.3124	-0.158	3.5369	0.7137	2.097	-0.2865	0.2245	-0.3177	-0.0015	0.0566	0.2342	0.5645	-0.3589	0.2299	0.3716	-0.1377	0.0949	0.1719	-0.008	0.2175	-9.8055	-27.7365	9.3305
16	4.5081	-0.6122	-0.7021	2.1098	0.5509	2.0307	-0.2489	-0.2163	-0.6437	0.1801	0.0871	-0.0906	0.9006	0.3276	0.1617	0.5519	0.1898	0.079	0.1721	0.0434	0.2414	17.5262	-38.336	5.7023

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	15 - 87
2	X-RAY DIFFRACTION	2	A	88 - 189
3	X-RAY DIFFRACTION	3	A	190 - 284
4	X-RAY DIFFRACTION	4	A	285 - 383
5	X-RAY DIFFRACTION	5	B	15 - 87
6	X-RAY DIFFRACTION	6	B	88 - 189
7	X-RAY DIFFRACTION	7	B	190 - 284
8	X-RAY DIFFRACTION	8	B	285 - 383
9	X-RAY DIFFRACTION	9	C	15 - 87
10	X-RAY DIFFRACTION	10	C	88 - 189
11	X-RAY DIFFRACTION	11	C	190 - 284
12	X-RAY DIFFRACTION	12	C	285 - 383
13	X-RAY DIFFRACTION	13	D	15 - 87
14	X-RAY DIFFRACTION	14	D	88 - 189
15	X-RAY DIFFRACTION	15	D	190 - 284
16	X-RAY DIFFRACTION	16	D	285 - 383

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