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Basic information

Entry
Database: PDB / ID: 2xyo
TitleStructural basis for a new tetracycline resistance mechanism relying on the TetX monooxygenase
ComponentsTETX2
KeywordsOXIDOREDUCTASE / 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
Flavin-dependent monooxygenase TetX / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Flavin-dependent monooxygenase
Similarity search - Component
Biological speciesBACTEROIDES THETAIOTAOMICRON (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsVolkers, G. / Palm, G.J. / Weiss, M.S. / Hinrichs, W.
CitationJournal: 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
DepositionNov 18, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2019Group: 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 1.4Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TETX2
B: TETX2
C: TETX2
D: TETX2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,41617
Polymers181,4134
Non-polymers4,00313
Water00
1
A: TETX2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3314
Polymers45,3531
Non-polymers9783
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TETX2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4235
Polymers45,3531
Non-polymers1,0704
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TETX2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3314
Polymers45,3531
Non-polymers9783
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: TETX2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3314
Polymers45,3531
Non-polymers9783
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
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 number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 3 / Auth seq-ID: 15 - 383 / Label seq-ID: 26 - 394

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
4DD
3CC

NCS oper:
IDCodeMatrixVector
1given(-0.92085, -0.01904, 0.38944), (0.02219, -0.99975, 0.00358), (0.38928, 0.01194, 0.92104)1.45742, 27.51358, -63.91325
2given(0.92002, 0.02744, -0.3909), (0.02562, -0.99962, -0.00988), (-0.39102, -0.00092, -0.92038)27.45115, 57.9208, 138.40414
3given(0.91982, 0.02069, -0.3918), (0.01471, -0.99972, -0.01827), (-0.39207, 0.01104, -0.91987)24.95196, 62.54359, 57.76976
4given(0.99994, -0.01087, -0.00125), (0.01088, 0.99991, 0.00835), (0.00116, -0.00837, 0.99996)29.34893, -4.61539, 75.14562
5given(-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
6given(-0.99996, -0.00841, 0.00171), (-0.00842, 0.9999, -0.01108), (-0.00161, -0.0111, -0.99994)29.16241, -28.63923, 75.16801

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Components

#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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity 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 growTemperature: 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.97784, 0.97838, 0.95369
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 27, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.977841
20.978381
30.953691
ReflectionResolution: 3→99 Å / Num. obs: 35742 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 53.8 Å2 / Rmerge(I) obs: 0.22 / Net I/σ(I): 11.7
Reflection shellResolution: 3→3.19 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.9 / % possible all: 98.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
Auto-Rickshawphasing
SHARPphasing
REFMAC5.5.0102refinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 3→149.64 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc 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.
RfactorNum. reflection% reflectionSelection details
Rfree0.29454 1783 5 %RANDOM
Rwork0.24905 ---
obs0.25132 33933 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.471 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å20 Å20.76 Å2
2--1.03 Å20 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 3→149.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11421 0 258 0 11679
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02212000
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.97816317
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.60751478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.69725.442588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.19151981
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3881558
X-RAY DIFFRACTIONr_chiral_restr0.1010.21775
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219186
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4151.57307
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.831211758
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.46534693
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3814.54549
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1464tight positional0.040.05
2B1464tight positional0.040.05
3C1464tight positional0.040.05
4D1464tight positional0.040.05
1A1390loose positional0.055
2B1390loose positional0.055
3C1390loose positional0.045
4D1390loose positional0.045
1A1464tight thermal0.070.5
2B1464tight thermal0.070.5
3C1464tight thermal0.060.5
4D1464tight thermal0.060.5
1A1390loose thermal0.0810
2B1390loose thermal0.0810
3C1390loose thermal0.0810
4D1390loose thermal0.0710
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 139 -
Rwork0.329 2425 -
obs--98.5 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
12.32940.8288-0.5513.1025-0.72092.9498-0.00330.14690.4616-0.09640.14120.314-0.4836-0.1248-0.1380.12780.0360.01010.03490.04750.112118.871614.923616.2262
22.60490.9912-0.17012.356-0.57742.57190.0205-0.10860.07220.09060.07710.03770.01970.0439-0.09750.0810.02850.02090.0916-0.06480.073424.42363.292419.3342
32.4380.80910.0261.6004-0.3942.8041-0.0253-0.2824-0.05740.12440.1726-0.19430.13670.1235-0.14730.03710.0562-0.00250.1164-0.01340.103426.14812.205126.027
43.1478-2.14930.767118.8354-3.20726.53670.1036-0.67240.4360.83360.66581.597-0.4749-0.2498-0.76940.1182-0.00530.13460.2816-0.1230.352523.347815.19833.8496
51.6582-0.7898-0.28672.94970.432.3418-0.0587-0.03940.3640.11510.058-0.3066-0.2961-0.00310.00070.1196-0.0290.00680.0503-0.03940.111110.047544.288258.454
62.6746-1.13220.13852.49080.47722.12240.01480.12830.0463-0.11470.0747-0.04940.00790.0255-0.08940.1103-0.04770.02180.08730.04720.06264.576932.593255.4686
71.0804-0.32190.13163.39820.07182.5271-0.00590.2154-0.1508-0.07960.00960.16460.0981-0.0421-0.00380.0141-0.03050.00540.1353-0.00880.16332.849731.419648.7801
85.0186-1.6452-0.263523.73867.58589.1126-0.13520.66050.2146-0.94890.6856-1.0098-0.15070.383-0.55040.14-0.00050.08680.27860.12640.18275.553844.37440.8272
93.47781.73380.41993.9384-0.04612.5332-0.0621-0.258-0.5204-0.161-0.1635-0.53770.50050.39350.22570.15610.14060.0570.29960.15590.185214.878512.603980.4977
102.33451.2945-0.7264.152-0.42952.57060.0578-0.5483-0.08320.244-0.1691-0.1657-0.09360.31690.11130.07430.0273-0.06160.3870.10450.114510.734324.158985.5175
111.37140.8565-0.56124.6994-0.25662.26340.093-0.7780.04010.4046-0.2024-0.0955-0.24970.43660.10940.1544-0.054-0.1110.52350.03410.244611.744925.261892.3655
121.97161.57-0.322912.9372-0.0924.90550.0301-0.787-0.63321.1830.1923-1.52280.27880.777-0.22240.19190.0611-0.13640.74130.25560.525817.651612.3998.4867
132.36051.2236-0.14283.5540.27832.6552-0.0798-0.2973-0.456-0.1057-0.208-0.47040.52520.62490.28780.17430.15080.02350.34250.15480.1972-14.23317.39295.5641
142.33291.1032-0.88163.9322-0.44712.97440.0045-0.5996-0.04670.2892-0.1268-0.1694-0.07020.50160.12230.08880.0336-0.07640.44190.06430.0953-18.286528.946310.6426
151.10220.6115-0.84645.0953-0.60642.60040.1348-0.78780.03650.4747-0.26750.0675-0.27450.59910.13270.2017-0.0583-0.09160.60520.03170.225-17.264130.013217.5023
162.8423.9103-1.522417.44180.76895.6801-0.0701-0.8811-0.40671.41230.3294-1.0410.31261.0054-0.25930.24290.1167-0.18420.86570.26280.4948-11.449217.056323.558
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 93
2X-RAY DIFFRACTION2A94 - 259
3X-RAY DIFFRACTION3A260 - 334
4X-RAY DIFFRACTION4A335 - 383
5X-RAY DIFFRACTION5B15 - 93
6X-RAY DIFFRACTION6B94 - 259
7X-RAY DIFFRACTION7B260 - 334
8X-RAY DIFFRACTION8B335 - 383
9X-RAY DIFFRACTION9D15 - 93
10X-RAY DIFFRACTION10D94 - 259
11X-RAY DIFFRACTION11D260 - 334
12X-RAY DIFFRACTION12D335 - 383
13X-RAY DIFFRACTION13C15 - 93
14X-RAY DIFFRACTION14C94 - 259
15X-RAY DIFFRACTION15C260 - 334
16X-RAY DIFFRACTION16C335 - 383

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