PDB-4a99: STRUCTURE OF THE TETRACYCLINE DEGRADING MONOOXYGENASE TETX IN COM...

ID or keywords:

Entry

Database: PDB / ID: 4a99

Title

STRUCTURE OF THE TETRACYCLINE DEGRADING MONOOXYGENASE TETX IN COMPLEX WITH MINOCYCLINE

Components

TETX2 PROTEIN

Keywords

FLAVOPROTEIN / TETRACYCLINE DEGRADATION / MONOOXYGENASE / FLAVIN

Function / homology

Function and homology information

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

Biological species

BACTEROIDES THETAIOTAOMICRON (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.18 Å

Authors

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

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Putative Dioxygen-Binding Sites and Recognition of Tigecycline and Minocycline in the Tetracycline-Degrading Monooxygenase Tetx
Authors: Volkers, G. / Damas, J.M. / Palm, G.J. / Panjikar, S. / Soares, C.M. / Hinrichs, W.

History

Deposition	Nov 25, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 12, 2012	Provider: repository / Type: Initial release
Revision 1.1	Aug 28, 2013	Group: Database references / Structure summary
Revision 1.2	Sep 11, 2013	Group: Database references
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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_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	4a99.cif.gz	605.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4a99.ent.gz	500.7 KB	Display	PDB format
PDBx/mmJSON format	4a99.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4a99_validation.pdf.gz	4.2 MB	Display	wwPDB validaton report
Full document	4a99_full_validation.pdf.gz	4.2 MB	Display
Data in XML	4a99_validation.xml.gz	66.8 KB	Display
Data in CIF	4a99_validation.cif.gz	89.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a9/4a99 ftp://data.pdbj.org/pub/pdb/validation_reports/a9/4a99	HTTPS FTP

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Related structure data

Related structure data	4a6nC 4guvC 2xdoS 2xyo 2y6q 2y6r S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3oz2-d 6ain-2 6ejj-1 5t8o-1 3dy0-d 3d7l-3 5t8p-2 3d7l-1 4axx-d 4au4-3 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

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: TETX2 PROTEIN

B: TETX2 PROTEIN

C: TETX2 PROTEIN

D: TETX2 PROTEIN

hetero molecules

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

1

A: TETX2 PROTEIN

hetero molecules

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

2

B: TETX2 PROTEIN

hetero molecules

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

3

C: TETX2 PROTEIN

hetero molecules

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

4

D: TETX2 PROTEIN

hetero molecules

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

Unit cell

Length a, b, c (Å)	68.878, 80.334, 86.627
Angle α, β, γ (deg.)	110.82, 90.27, 93.39
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: MIY / End label comp-ID: MIY / Refine code: 1 / Auth seq-ID: 13 - 391 / Label seq-ID: 23

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A - F
2	B	B - J
3	C	C - O
4	D	D - U

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(0.99997, -0.006106, 0.004676), (-0.00611, -0.999981, 0.000783), (0.004671, -0.000811, -0.999989)	-29.49111, 35.78112, 54.88291
3	given	(-0.998974, -0.004699, 0.045039), (0.009738, 0.94904, 0.315007), (-0.044224, 0.315122, -0.94802)	-34.63551, 7.59569, 61.91875
4	given	(-0.998902, 0.007645, -0.046223), (0.007329, -0.948953, -0.315332), (-0.046275, -0.315325, 0.947855)	2.59157, -17.68111, -2.67194

#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-MIY / (4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE / MINOCYCLINE Mass: 457.476 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂₃H₂₇N₃O₇ / Comment: medication, antibiotic*YM
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 640 / 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: 50 % / 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: 14.2 / Wavelength: 0.91841
Detector	Type: MARRESEARCH MAR165 / Detector: CCD / Date: Apr 28, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.91841 Å / Relative weight: 1
Reflection	Resolution: 2.18→80.94 Å / Num. obs: 86443 / % possible obs: 95.4 % / Observed criterion σ(I): 2 / Redundancy: 3.75 % / R_merge(I) obs: 0.1 / Net I/σ(I): 11.86
Reflection shell	Resolution: 2.18→2.31 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.62 / Mean I/σ(I) obs: 2.37 / % possible all: 80.4

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Processing

Software

Name	Version	Classification
REFMAC	5.6.0116	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XDO

2xdo

Resolution: 2.18→80.94 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.924 / SU B: 11.247 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23476	4301	5 %	RANDOM
R_work	0.18462	-	-	-
obs	0.18713	82141	95.52 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 53.132 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.07 Å²	0.31 Å²	0.03 Å²
2-	-	0.99 Å²	1.27 Å²
3-	-	-	-1.11 Å²

Refinement step

Cycle: LAST / Resolution: 2.18→80.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11496	0	526	640	12662

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.02	12288
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.918	2.032	16770
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.155	5	1462
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.235	25.624	585
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.548	15	1991
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.034	15	52
X-RAY DIFFRACTION	r_chiral_restr	0.149	0.2	1837
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	9340
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
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 / Number: 2923 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	tight positional	0.09	0.05
2	B	tight positional	0.1	0.05
3	C	tight positional	0.07	0.05
4	D	tight positional	0.08	0.05
1	A	tight thermal	3.79	0.5
2	B	tight thermal	3.37	0.5
3	C	tight thermal	3.44	0.5
4	D	tight thermal	3.52	0.5

LS refinement shell

Resolution: 2.179→2.236 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.313	197	-
R_work	0.266	3857	-
obs	-	-	60.54 %

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	1.1703	0.3914	0.8075	1.2534	-0.1396	2.3374	0.0209	-0.0441	-0.0276	-0.029	0.019	0.1306	0.0379	-0.1967	-0.0399	0.1078	-0.0139	-0.0029	0.1139	0.0073	0.1808	-15.8467	-0.8688	14.9502
2	1.1814	0.3839	0.5038	1.3401	-0.0741	1.3459	0.0527	0.0533	0.0832	-0.1663	-0.0106	0.0349	-0.0106	-0.1149	-0.0421	0.0978	0.01	0.0065	0.0925	-0.0169	0.0904	-11.0381	4.657	9.8319
3	3.1315	-0.0274	-0.6262	2.6076	-0.4711	2.7089	0.0852	0.2144	0.1119	-0.179	-0.0978	-0.3485	-0.0175	0.345	0.0126	0.0738	-0.0014	0.0205	0.168	-0.014	0.2478	13.6145	4.8482	15.1169
4	3.3257	-0.1011	0.2074	2.4816	-0.072	1.3711	-0.0085	-0.1498	0.3325	0.16	0.0338	0.1413	-0.2998	-0.0349	-0.0253	0.1448	0.0583	0.008	0.0882	-0.0199	0.1851	-13.6582	16.3194	14.7415
5	1.5212	-0.3864	-0.6651	1.4733	-0.6151	2.9048	0.0233	0.0271	0.0229	0.1007	0.0317	0.142	-0.0492	-0.1528	-0.055	0.1176	-0.0086	0.0007	0.0939	-0.0098	0.1594	13.8356	36.4137	40.8444
6	1.2565	-0.3486	-0.4359	1.3806	-0.0244	1.4823	0.0733	-0.0655	-0.0873	0.2053	-0.0107	0.0297	0.0697	-0.0621	-0.0626	0.1202	-0.0109	-0.001	0.0947	-0.0061	0.0823	18.605	30.7309	46.0363
7	2.9884	0.0888	0.5018	2.2654	-0.0362	2.3637	0.0848	-0.2711	-0.1438	0.2248	-0.135	-0.2989	0.0656	0.351	0.0502	0.0861	0.0221	-0.0101	0.2185	0.0108	0.2501	43.2576	30.4364	40.5855
8	3.3688	0.1175	-0.3183	2.4943	-0.396	1.6924	-0.0093	0.0921	-0.3359	-0.1163	0.0074	0.1066	0.359	-0.0808	0.002	0.1826	-0.0744	-0.0127	0.0896	-0.0237	0.1828	15.94	19.2164	40.8291
9	1.7706	0.2293	0.5828	1.6161	0.059	1.9284	-0.0479	0.0744	-0.0808	-0.085	0.046	-0.2784	0.0053	0.2887	0.0019	0.1879	-0.0694	0.0014	0.1953	-0.0173	0.1415	-14.8768	-23.5562	44.1826
10	1.7614	0.0356	0.4743	1.6206	0.0381	1.6414	0.0254	-0.0534	0.0052	0.1363	0.0061	-0.088	-0.0797	0.208	-0.0315	0.1725	-0.0876	-0.0101	0.1405	0.0195	0.068	-19.5189	-20.083	51.1694
11	3.6747	0.5368	-0.6007	3.2759	0.2979	3.4584	-0.0939	-0.2735	0.0902	0.1757	-0.0668	0.322	-0.1043	-0.221	0.1607	0.1675	0.015	-0.0095	0.1545	-0.0133	0.2441	-44.2907	-17.9176	46.3949
12	2.3701	0.4492	0.2842	2.3216	0.268	1.2607	0.0519	-0.0899	0.219	0.0649	-0.0792	-0.0622	-0.3827	0.1447	0.0273	0.2592	-0.1212	-0.0179	0.1569	-0.0228	0.12	-16.9498	-7.3433	49.9869
13	1.7602	-0.2316	-0.8331	1.5751	-0.2475	2.3449	-0.0513	-0.1188	0.1058	0.0242	0.0477	-0.2524	0.0772	0.3273	0.0036	0.1833	0.0543	0.0029	0.1685	-0.0331	0.152	19.6207	-22.1268	11.5224
14	1.9419	-0.1299	-0.3521	1.3849	-0.0181	1.5968	-0.0213	0.0424	-0.0423	-0.1291	0.0105	-0.0787	0.1186	0.1873	0.0108	0.1761	0.0548	0.0237	0.0984	0.0025	0.0711	14.9725	-25.5918	4.3266
15	3.8334	-0.5635	0.3786	3.2922	0.0949	2.6634	-0.0705	0.242	-0.1887	-0.1542	0.012	0.2873	0.1529	-0.2191	0.0586	0.1606	-0.0202	0.0118	0.1506	-0.0193	0.2467	-9.8055	-27.7365	9.3305
16	3.8941	-0.3118	-0.7112	2.0492	0.2984	1.038	-0.0443	0.0346	-0.3632	-0.0354	0.0173	-0.0698	0.4015	0.1252	0.0269	0.2479	0.0859	0.0328	0.1188	-0.0096	0.1302	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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