PDB-2y6q: Structure of the TetX monooxygenase in complex with the substrate...

ID or keywords:

Entry

Database: PDB / ID: 2y6q

Title

Structure of the TetX monooxygenase in complex with the substrate 7- Iodtetracycline

Components

TETX2 PROTEIN

Keywords

OXIDOREDUCTASE / ANTIBIOTIC RESISTANCE / FLAVIN / 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 /

MOLECULAR REPLACEMENT / Resolution: 2.37 Å

Authors

Volkers, G. / Palm, G.J. / Weiss, M.S. / 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	Jan 25, 2011	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	Dec 20, 2023	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_ncs_dom_lim / 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_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_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	2y6q.cif.gz	599.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2y6q.ent.gz	496.8 KB	Display	PDB format
PDBx/mmJSON format	2y6q.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y6/2y6q ftp://data.pdbj.org/pub/pdb/validation_reports/y6/2y6q	HTTPS FTP

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Related structure data

Related structure data	2xdoSC 2xyoC 2y6rC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4a99-2 2y6r-2 3v3n-1 3v3o-2 3p9u-2 4a6n-1 4guv-1 3v3n-4 3v3o-4 4a99-3 3v3o-1 4guv-4 2y6r-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

2xdoSC

2xyoC

2y6rC

S: Starting model for refinement

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

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

1

A: TETX2 PROTEIN

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 PROTEIN

hetero molecules

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

3

C: TETX2 PROTEIN

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 PROTEIN

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)	68.700, 79.960, 88.000
Angle α, β, γ (deg.)	111.10, 90.41, 92.96
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:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 3 / Auth seq-ID: 14 - 383 / Label seq-ID: 24 - 393

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B
3	C	C
4	D	D

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.99944, 0.00913, 0.03216), (0.01913, 0.94503, 0.32641), (-0.02741, 0.32684, -0.94468)	-33.6823, 7.05483, 63.66823
2	given	(-0.99969, -0.00657, 0.0242), (-0.00184, -0.94328, -0.332), (0.02501, -0.33194, 0.94297)	-4.07829, 28.36502, -7.86302
3	given	(-0.9996, 0.01626, -0.02305), (0.00764, 0.94273, 0.33348), (0.02715, 0.33317, -0.94247)	32.23575, 52.4534, 59.00922
4	given	(-0.99952, 0.0005, -0.03093), (0.00967, -0.94471, -0.32777), (-0.02939, -0.32791, 0.94425)	2.35544, -18.02945, -2.98467
5	given	(0.99985, -0.01742, 0.00245), (-0.01744, -0.99983, 0.00535), (0.00235, -0.00539, -0.99998)	29.56806, 34.48912, 55.92127

#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-I7T / 7-IODOTETRACYCLINE Mass: 540.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₁IN₂O₇
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.47 Å³/Da / Density % sol: 50.28 % / Description: NONE
Crystal grow	pH: 7 / Details: 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 SX-165 / Detector: CCD / Date: Nov 23, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.918 Å / Relative weight: 1
Reflection	Resolution: 2.37→51.98 Å / Num. obs: 66166 / % possible obs: 93.5 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / B_iso Wilson estimate: 49.7 Å² / R_merge(I) obs: 0.09 / Net I/σ(I): 7.3
Reflection shell	Resolution: 2.37→2.5 Å / Redundancy: 2.5 % / R_merge(I) obs: 0.49 / Mean I/σ(I) obs: 2.1 / % possible all: 69.6

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0110	refinement
XDS		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XDO

2xdo

Resolution: 2.37→51.98 Å / Cor.coef. F_o:F_c: 0.936 / Cor.coef. F_o:F_c free: 0.926 / SU B: 17.038 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.481 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23776	3314	5 %	RANDOM
R_work	0.21838	-	-	-
obs	0.21937	62850	93.46 %	-

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 mean: 44.735 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.38 Å²	-0.02 Å²	-0.83 Å²
2-	-	0.4 Å²	0.4 Å²
3-	-	-	-3.52 Å²

Refinement step

Cycle: LAST / Resolution: 2.37→51.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11346	0	396	197	11939

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.022	12018
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.02	7765
X-RAY DIFFRACTION	r_angle_refined_deg	1.825	1.994	16400
X-RAY DIFFRACTION	r_angle_other_deg	1.147	3	19035
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.909	5	1468
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.437	25.674	571
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.537	15	1905
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.016	15	48
X-RAY DIFFRACTION	r_chiral_restr	0.128	0.2	1799
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	13398
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	2283
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	0.711	1.5	7300
X-RAY DIFFRACTION	r_mcbond_other	0.172	1.5	2980
X-RAY DIFFRACTION	r_mcangle_it	1.322	2	11724
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.179	3	4718
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.479	4.5	4672
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	2129	tight positional	0.05	0.05
2	B	2129	tight positional	0.06	0.05
3	C	2129	tight positional	0.05	0.05
4	D	2129	tight positional	0.05	0.05
1	A	2530	loose positional	0.06	5
2	B	2530	loose positional	0.06	5
3	C	2530	loose positional	0.06	5
4	D	2530	loose positional	0.06	5
1	A	2129	tight thermal	0.16	0.5
2	B	2129	tight thermal	0.16	0.5
3	C	2129	tight thermal	0.13	0.5
4	D	2129	tight thermal	0.12	0.5
1	A	2530	loose thermal	0.15	10
2	B	2530	loose thermal	0.15	10
3	C	2530	loose thermal	0.12	10
4	D	2530	loose thermal	0.13	10

LS refinement shell

Resolution: 2.37→2.431 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.349	146	-
R_work	0.372	3158	-
obs	-	-	63.26 %

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	2.4048	0.1095	0.9578	3.1855	-0.2436	3.96	0.2639	-0.1784	-0.0669	0.0287	-0.0776	0.4155	0.3189	-0.427	-0.1863	0.0501	-0.0473	0.0143	0.059	-0.0043	0.1582	-15.8467	-0.8688	14.9502
2	2.3516	0.1362	1.0623	2.3916	-0.0428	2.635	0.0967	-0.0322	0.0639	-0.1839	-0.0538	0.3424	0.0417	-0.2501	-0.0429	0.0616	-0.0168	0.0107	0.0429	-0.0199	0.08	-11.0381	4.657	9.8319
3	4.0806	0.434	-0.4437	4.7374	0.0181	4.1477	0.1386	0.226	0.052	-0.1548	-0.0813	-0.6144	0.1596	0.6597	-0.0573	0.0354	0.0176	0.0296	0.1779	-0.0338	0.1568	13.6145	4.8482	15.1169
4	5.0389	-0.4119	0.6977	3.7796	-0.1381	3.2354	0.037	-0.3442	0.5086	0.3079	-0.0242	0.5304	-0.492	-0.3149	-0.0128	0.104	0.0415	0.0618	0.081	-0.0325	0.2031	-13.6582	16.3194	14.7415
5	3.0614	-0.1578	-0.7645	2.9592	-0.6819	5.3669	0.1942	0.1894	0.2768	-0.0875	-0.1096	0.4985	-0.2968	-0.5143	-0.0846	0.0297	0.0442	-0.0092	0.0741	-0.035	0.1703	13.8356	36.4137	40.8444
6	2.9553	-0.1864	-1.1958	3.0458	0.2288	3.0229	0.154	0.0896	-0.0232	0.1647	-0.097	0.3139	-0.019	-0.3248	-0.057	0.022	0.0087	0.0073	0.1035	-0.0394	0.058	18.605	30.7309	46.0363
7	4.628	-0.2331	-0.3992	5.7182	-0.1587	3.9404	0.0736	-0.322	-0.1262	0.0354	-0.0897	-0.7295	-0.0968	0.5806	0.016	0.0205	0.006	0.006	0.2016	-0.0366	0.1936	43.2576	30.4364	40.5855
8	5.7915	0.1393	-0.863	4.0279	-0.1486	2.4426	0.1276	0.3037	-0.3682	-0.2997	-0.1454	0.4083	0.569	-0.4092	0.0178	0.1784	-0.0925	-0.0265	0.1229	-0.0765	0.1382	15.94	19.2164	40.8291
9	2.9718	0.3981	1.1093	3.6844	-0.165	4.8518	0.0317	0.3826	-0.0064	-0.4292	0.0243	-0.6624	-0.3162	0.7928	-0.0559	0.1834	-0.1362	0.1198	0.2315	-0.0669	0.2337	-14.8768	-23.5562	44.1826
10	3.3822	0.2523	1.109	2.8038	0.3372	3.3511	-0.1424	0.1699	0.2131	-0.0261	0.1501	-0.3444	-0.5166	0.5117	-0.0077	0.1962	-0.1409	0.0279	0.1207	-0.0154	0.1039	-19.5189	-20.083	51.1694
11	5.5339	0.2633	-0.6995	5.4196	0.9406	4.3906	-0.1546	-0.1329	0.24	-0.1388	-0.1031	0.5692	-0.4251	-0.6615	0.2578	0.3211	0.0867	-0.0751	0.1962	0.0106	0.2893	-44.2907	-17.9176	46.3949
12	6.216	0.6731	1.0016	3.4942	0.5399	2.5575	-0.0549	0.1944	0.9556	-0.2908	0.0276	-0.311	-1.1045	0.437	0.0273	0.5586	-0.2234	-0.0048	0.2161	0.0356	0.333	-16.9498	-7.3433	49.9869
13	3.0567	-0.0055	-0.4897	3.4856	-0.1786	5.3117	0.0465	-0.4401	-0.1054	0.4813	0.1299	-0.6356	0.3987	0.785	-0.1764	0.2994	0.1699	-0.0905	0.2252	-0.054	0.205	19.6207	-22.1268	11.5224
14	3.2572	-0.055	-0.9312	2.9147	0.4007	3.3223	-0.0947	-0.1151	-0.2565	0.0941	0.1901	-0.4035	0.4579	0.4833	-0.0955	0.2626	0.1508	-0.0354	0.1115	-0.0447	0.1112	14.9725	-25.5918	4.3266
15	5.292	-0.2044	-0.3074	5.1005	0.4743	4.5417	-0.261	0.3039	-0.2697	0.1197	-0.0005	0.4429	0.556	-0.6482	0.2615	0.4068	-0.1422	0.0864	0.1806	-0.0125	0.2648	-9.8055	-27.7365	9.3305
16	5.4141	-0.3638	-0.7216	2.7507	0.3678	2.2735	-0.0171	-0.1248	-1.1007	0.2231	0.0315	-0.3126	1.0391	0.466	-0.0143	0.689	0.2217	-0.0248	0.2034	0.0159	0.3762	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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