PDB-4a6n: STRUCTURE OF THE TETRACYCLINE DEGRADING MONOOXYGENASE TETX IN COM...

ID or keywords:

Entry

Database: PDB / ID: 4a6n

Title

STRUCTURE OF THE TETRACYCLINE DEGRADING MONOOXYGENASE TETX IN COMPLEX WITH TIGECYCLINE

Components

(TETX2 PROTEIN) x 2

Keywords

OXIDOREDUCTASE / ANTIBIOTIC RESISTANCE

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: 2.3 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 7, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 21, 2012	Provider: repository / Type: Initial release
Revision 1.1	Aug 28, 2013	Group: Database references
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 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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Download

PDBx/mmCIF format	4a6n.cif.gz	597.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4a6n.ent.gz	496.1 KB	Display	PDB format
PDBx/mmJSON format	4a6n.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4a6n_validation.pdf.gz	2.4 MB	Display	wwPDB validaton report
Full document	4a6n_full_validation.pdf.gz	2.4 MB	Display
Data in XML	4a6n_validation.xml.gz	60.1 KB	Display
Data in CIF	4a6n_validation.cif.gz	78.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a6/4a6n ftp://data.pdbj.org/pub/pdb/validation_reports/a6/4a6n	HTTPS FTP

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Related structure data

Related structure data	4a99C 4guvC 2xdoS 2xyo 2y6q 2y6r S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4guv-2 3v3o-1 3v3o-3 3v3n-4 3p9u-4 6wg9-2 2y6r-2 4a99-3 2xdo-1 2y6q-2 1lq8-4 5frx-d 3p9u-2 3v3o-2 4a99-2 2y6q-1 6sw2-d 1cc4-d 4guv-1 4guv-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

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
46.5 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
46.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	68.880, 80.790, 87.650
Angle α, β, γ (deg.)	110.84, 89.84, 93.63
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	1	A	12 - 388
2	1	1	1	B	12 - 388
3	1	1	1	C	12 - 388
4	1	1	1	D	12 - 388

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(0.99996, -0.008901, -0.000315), (-0.008902, -0.999949, -0.004692), (-0.000273, 0.004694, -0.999989)	-29.18224, 36.17907, 55.46955
3	given	(-0.99925, 0.000258, 0.03872), (0.012607, 0.947654, 0.319051), (-0.036611, 0.3193, -0.946946)	-33.80432, 7.34374, 63.09957
4	given	(-0.999387, 0.001019, -0.034994), (0.010203, -0.947705, -0.318983), (-0.033489, -0.319145, 0.947114)	2.71399, -17.90279, -2.69097

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Protein , 2 types, 4 molecules ABCD

#1: Protein	TETX2 PROTEIN / TETX Mass: 44703.461 Da / Num. of mol.: 1 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: Protein	TETX2 PROTEIN / TETX Mass: 44703.395 Da / Num. of mol.: 3 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

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Non-polymers , 4 types, 229 molecules

#3: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#4: Chemical	ChemComp-T1C / TIGECYCLINE Mass: 587.665 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₉H₄₁N₅O₈
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.44 Å³/Da / Density % sol: 49.6 % / 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: MARMOSAIC 225 mm CCD / 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: 2.3→81.897 Å / Num. obs: 75167 / % possible obs: 96 % / Redundancy: 3.9 % / R_merge(I) obs: 0.088 / Net I/σ(I): 9.1
Reflection shell	Resolution: 2.3→2.42 Å / Redundancy: 3.9 % / R_merge(I) obs: 0.622 / Mean I/σ(I) obs: 2 / % possible all: 95.5

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XDO

2xdo

Resolution: 2.3→81.9 Å / Cor.coef. F_o:F_c: 0.939 / Cor.coef. F_o:F_c free: 0.913 / SU B: 15.307 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.377 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26024	3769	5 %	RANDOM
R_work	0.21821	-	-	-
obs	0.22033	71396	96.04 %	-

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: 61.598 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.08 Å²	-0.62 Å²	0.64 Å²
2-	-	0.44 Å²	0.66 Å²
3-	-	-	-2.13 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→81.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11496	0	435	210	12141

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.02	12184
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.02	7989
X-RAY DIFFRACTION	r_angle_refined_deg	1.759	1.998	16599
X-RAY DIFFRACTION	r_angle_other_deg	1.114	3.002	19497
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.33	5	1462
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.665	25.616	584
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.495	15	1993
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.135	15	52
X-RAY DIFFRACTION	r_chiral_restr	0.127	0.2	1814
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	13470
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	2334
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: 4741 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	tight positional	0.05	0.05
2	B	tight positional	0.05	0.05
3	C	tight positional	0.04	0.05
4	D	tight positional	0.04	0.05
1	A	tight thermal	6.35	0.5
2	B	tight thermal	6.11	0.5
3	C	tight thermal	6.02	0.5
4	D	tight thermal	6.41	0.5

LS refinement shell

Resolution: 2.3→2.36 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.327	289	-
R_work	0.276	5205	-
obs	-	-	95.51 %

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	1.127	0.4878	1.1602	1.842	-0.2849	1.8877	0.0474	-0.1262	-0.0549	0.0457	-0.0163	0.2186	0.0119	-0.2317	-0.0311	0.0275	-0.0219	-0.0005	0.1037	0.0224	0.1814	-15.8467	-0.8688	14.9502
2	1.5754	0.3346	0.6663	1.4163	0.3563	1.6875	0.0443	0.0122	0.032	-0.0759	-0.002	0.1451	-0.0485	-0.1326	-0.0422	0.0296	-0.002	-0.0127	0.0561	-0.0055	0.0619	-11.0381	4.657	9.8319
3	2.1508	0.4658	-0.291	2.6491	0.0555	1.8458	0.0395	0.2107	0.0711	-0.1671	0.1299	-0.2295	-0.1125	0.2722	-0.1694	0.0534	-0.0344	-0.0158	0.1653	-0.0328	0.1791	13.6145	4.8482	15.1169
4	3.5278	-0.6068	0.462	2.3594	-0.0728	1.3536	-0.0329	-0.179	0.2997	0.1243	-0.0151	0.2356	-0.391	-0.1116	0.048	0.1353	0.0546	0.0195	0.0907	-0.0274	0.1456	-13.6582	16.3194	14.7415
5	1.6181	-0.3232	-0.8407	1.33	-0.536	2.1409	0.0184	0.1728	0.0571	-0.0226	-0.0853	0.2507	-0.0909	-0.2816	0.0669	0.0569	0.0259	-0.0104	0.0823	-0.0086	0.1543	13.8356	36.4137	40.8444
6	1.6264	-0.1109	-0.731	1.563	0.356	1.4965	0.0767	0.0338	0.0056	0.1198	-0.0446	0.0997	0.0813	-0.109	-0.032	0.028	0.0125	-0.0028	0.0753	-0.0189	0.0357	18.605	30.7309	46.0363
7	2.6494	-0.46	0.4573	2.7202	0.1772	2.3419	0.0617	-0.2758	-0.1566	0.1492	0.0529	-0.3295	0.0559	0.3451	-0.1146	0.0242	0.0235	-0.0043	0.1785	-0.0139	0.2091	43.2576	30.4364	40.5855
8	3.3068	0.4443	-0.8272	2.2357	-0.0966	1.9685	-0.0404	0.1638	-0.2327	-0.0442	-0.0583	0.1229	0.3756	-0.1619	0.0987	0.118	-0.0648	-0.011	0.086	-0.0568	0.1431	15.94	19.2164	40.8291
9	2.4288	0.0769	0.6617	1.6788	0.0751	1.9839	-0.058	0.1679	0.0028	-0.1297	0.0578	-0.3324	-0.1418	0.2096	0.0002	0.1464	-0.0962	0.036	0.075	-0.0188	0.0906	-14.8768	-23.5562	44.1826
10	1.9168	0.0745	0.6198	1.5609	-0.0589	1.5425	-0.0886	0.0225	0.0549	0.0504	0.1002	-0.1758	-0.2876	0.1844	-0.0115	0.1379	-0.0844	-0.0301	0.064	0.0021	0.033	-19.5189	-20.083	51.1694
11	3.7896	0.5531	-0.1207	2.9752	0.0657	1.8845	-0.0843	-0.1703	0.221	0.1453	-0.0228	0.4349	-0.2824	-0.2413	0.1071	0.1647	0.083	-0.0426	0.0845	0.0072	0.1673	-44.2907	-17.9176	46.3949
12	4.366	0.6208	1.0518	2.372	0.5269	1.6114	-0.0104	0.0495	0.426	-0.1039	0.0119	-0.0771	-0.6213	0.2313	-0.0015	0.3591	-0.151	-0.0238	0.0697	0.0339	0.1261	-16.9498	-7.3433	49.9869
13	2.27	0.1722	-0.8712	1.9849	-0.0687	1.7272	-0.0236	-0.1895	-0.1016	0.131	0.0332	-0.271	0.1039	0.3153	-0.0096	0.144	0.1057	-0.0522	0.1168	-0.0224	0.0595	19.6207	-22.1268	11.5224
14	2.1817	0.1443	-0.6609	1.6486	0.1625	1.61	-0.0903	-0.0195	-0.1506	0.0063	0.1177	-0.2587	0.3027	0.2127	-0.0275	0.1358	0.0764	-0.0004	0.0527	-0.0209	0.0496	14.9725	-25.5918	4.3266
15	3.9569	0.0406	0.6157	2.808	0.4895	1.995	-0.2271	0.1623	-0.1618	-0.0591	0.0911	0.2327	0.2706	-0.2261	0.136	0.1977	-0.0931	0.0871	0.0688	-0.005	0.1447	-9.8055	-27.7365	9.3305
16	3.3485	0.4939	-0.3735	2.0579	0.6457	1.5077	0.0218	-0.1015	-0.4802	0.2138	-0.0173	-0.1478	0.7097	0.2367	-0.0044	0.3768	0.1374	0.0056	0.0645	0.0398	0.1476	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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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi