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- PDB-2y6r: Structure of the TetX monooxygenase in complex with the substrate... -

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Basic information

Entry
Database: PDB / ID: 2y6r
TitleStructure of the TetX monooxygenase in complex with the substrate 7- chlortetracycline
ComponentsTETX2 PROTEIN
KeywordsOXIDOREDUCTASE / 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
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
7-CHLOROTETRACYCLINE / FLAVIN-ADENINE DINUCLEOTIDE / Flavin-dependent monooxygenase
Similarity search - Component
Biological speciesBACTEROIDES THETAIOTAOMICRON (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsVolkers, G. / Palm, G.J. / Weiss, M.S. / Wright, G.D. / 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
DepositionJan 25, 2011Deposition 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 1.3Dec 20, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)184,46323
Polymers178,3494
Non-polymers6,11419
Water1,69394
1
A: TETX2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1406
Polymers44,5871
Non-polymers1,5535
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TETX2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1406
Polymers44,5871
Non-polymers1,5535
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TETX2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0445
Polymers44,5871
Non-polymers1,4574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: TETX2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1406
Polymers44,5871
Non-polymers1,5535
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.416, 78.870, 86.609
Angle α, β, γ (deg.)110.99, 90.27, 92.87
Int Tables number1
Space group name H-MP1
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: 25 - 393

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

NCS oper:
IDCodeMatrixVector
1given(-0.9984, -0.00149, 0.05661), (0.0178, 0.94075, 0.33862), (-0.05376, 0.33909, -0.93922)-34.55771, 5.96727, 61.64372
2given(0.99997, -0.00702, 0.00294), (-0.00703, -0.99996, 0.00542), (0.00291, -0.00544, -0.99998)33.5425, -44.79966, 54.77277
3given(-0.99888, -0.00871, 0.04644), (-0.00733, -0.94236, -0.33451), (0.04668, -0.33447, 0.94125)-4.92228, 28.5899, -6.93168
4given(0.99991, -0.01055, 0.00769), (-0.01051, -0.99993, -0.00531), (0.00774, 0.00523, -0.99996)29.24026, 34.51287, 54.93652
5given(-0.99818, 0.0123, -0.05907), (0.00877, -0.93898, -0.34386), (-0.0597, -0.34375, 0.93716)2.61017, -17.69847, -3.00693
6given(-0.99868, -0.00143, 0.05143), (0.01612, 0.9406, 0.33912), (-0.04886, 0.3395, -0.93934)29.0364, -69.25974, 38.30962

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Components

#1: Protein
TETX2 PROTEIN


Mass: 44587.254 Da / Num. of mol.: 4 / Fragment: FAD-BINDING DOMAIN, RESIDUES 11-388 / Mutation: YES
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-CTC / 7-CHLOROTETRACYCLINE


Mass: 478.880 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H23ClN2O8 / Comment: antibiotic*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 94 TO ALA ENGINEERED RESIDUE IN CHAIN A, LYS 95 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, GLU 94 TO ALA ENGINEERED RESIDUE IN CHAIN A, LYS 95 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 94 TO ALA ENGINEERED RESIDUE IN CHAIN B, LYS 95 TO ALA ENGINEERED RESIDUE IN CHAIN C, GLU 94 TO ALA ENGINEERED RESIDUE IN CHAIN C, LYS 95 TO ALA ENGINEERED RESIDUE IN CHAIN D, GLU 94 TO ALA ENGINEERED RESIDUE IN CHAIN D, LYS 95 TO ALA

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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: 2.36 Å3/Da / Density % sol: 47.87 % / Description: NONE
Crystal growpH: 7 / Details: pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.918
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: Nov 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 3.09→48.33 Å / Num. obs: 29712 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 56.1 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.6
Reflection shellResolution: 3.09→3.21 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.1 / % possible all: 92.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
XDSdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XDO

2xdo


Resolution: 3.1→48.33 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.881 / SU B: 54.13 / SU ML: 0.461 / Cross valid method: THROUGHOUT / ESU R Free: 0.524 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25616 1493 5 %RANDOM
Rwork0.22509 ---
obs0.22672 28232 98.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.959 Å2
Baniso -1Baniso -2Baniso -3
1-5.37 Å2-0.18 Å2-0.37 Å2
2---3.44 Å2-2.55 Å2
3----3.77 Å2
Refinement stepCycle: LAST / Resolution: 3.1→48.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11265 0 399 94 11758
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02211927
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.99316283
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59751456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.15925.514564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.957151874
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.011551
X-RAY DIFFRACTIONr_chiral_restr0.0960.21786
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219145
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_it0.4371.57254
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.821211645
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.1234673
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0134.54636
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
1A1447tight positional0.040.05
2B1447tight positional0.040.05
3C1447tight positional0.040.05
4D1447tight positional0.040.05
1A1331loose positional0.055
2B1331loose positional0.055
3C1331loose positional0.045
4D1331loose positional0.055
1A1447tight thermal0.070.5
2B1447tight thermal0.070.5
3C1447tight thermal0.060.5
4D1447tight thermal0.060.5
1A1331loose thermal0.0810
2B1331loose thermal0.0810
3C1331loose thermal0.0710
4D1331loose thermal0.0710
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 106 -
Rwork0.294 2091 -
obs--98.48 %
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)
14.2522-0.14352.63962.2896-1.82526.83370.0775-0.1474-0.45370.0487-0.05850.54160.5142-0.1695-0.0190.0708-0.03390.0790.0281-0.01060.2845-15.8467-0.868814.9502
23.8630.16662.26163.44860.80174.51740.1393-0.08560.22030.001-0.05080.494-0.0074-0.3367-0.08840.04650.02120.0380.1217-0.00030.1179-11.03814.6579.8319
33.8384-1.1436-0.9758.4114-1.35565.0696-0.07310.16820.1896-0.20380.2427-0.94490.40730.5458-0.16960.13120.0115-0.09130.2041-0.09070.219813.61454.848215.1169
47.32591.11681.6154.81071.28982.59930.2537-0.24480.60230.4955-0.28270.3419-0.387-0.17060.02910.39670.11580.08860.1002-0.00920.2036-13.658216.319414.7415
54.30580.0485-0.61753.8931-1.85227.41790.042-0.03510.492-0.5251-0.08050.4631-0.881-0.2270.03850.32570.0467-0.08620.0483-0.04780.137913.835636.413740.8444
63.91020.474-1.98463.76370.24414.22340.1254-0.0612-0.051-0.0924-0.03520.2026-0.0525-0.4549-0.09020.2186-0.0664-0.0650.16220.01380.02918.60530.730946.0363
76.2942.55380.63165.979-2.53476.77060.1235-0.1925-0.4229-0.28410.0001-0.999-0.39740.8303-0.12360.2307-0.08530.15990.3105-0.11920.249643.257630.436440.5855
87.6164-0.8192-1.54614.87461.80392.50580.42530.2816-0.5094-0.2651-0.34510.17110.3532-0.2259-0.08030.3397-0.0482-0.1450.2076-0.02410.101115.9419.216440.8291
92.79292.87773.17524.97920.9217.9125-0.27560.458-0.3856-0.91330.4613-0.8602-0.22810.6326-0.18570.4729-0.0870.24820.2761-0.09660.2998-14.8768-23.556244.1826
104.03220.43951.82225.28770.04373.9678-0.09170.18180.3847-0.54340.0948-0.4879-0.40040.4866-0.00310.1998-0.09170.03140.23960.03730.1833-19.5189-20.08351.1694
115.72782.8777-0.43887.64972.2029.0431-0.01840.05450.7147-1.2495-0.37691.5022-0.5268-1.1150.39530.37650.1796-0.41730.3321-0.07990.5987-44.2907-17.917646.3949
123.9336-0.52871.39086.3566-0.23921.3522-0.0379-0.14310.9672-1.26160.1233-0.3835-1.13430.362-0.08541.2971-0.39490.33310.308-0.060.4846-16.9498-7.343349.9869
135.9941-2.91-2.5235.50890.22328.3737-0.1992-0.53890.47171.08390.3654-0.84240.13610.773-0.16620.32680.0623-0.16630.1729-0.1340.202519.6207-22.126811.5224
143.6845-0.1948-1.50494.6486-0.10863.2806-0.0352-0.0567-0.28090.28460.177-0.45290.36390.4386-0.14180.21010.0947-0.01220.22420.01090.136914.9725-25.59184.3266
157.9781-2.21440.9398.8542.04528.1814-0.27790.2228-0.67580.9495-0.16171.11990.5201-0.74290.43960.3762-0.13950.30240.1581-0.00240.3693-9.8055-27.73659.3305
165.98511.0967-1.97615.3235-0.20431.2307-0.00190.0563-1.00990.69320.1614-0.74110.97520.4006-0.15951.15320.4361-0.43110.2979-0.16140.640217.5262-38.3365.7023
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 87
2X-RAY DIFFRACTION2A88 - 189
3X-RAY DIFFRACTION3A190 - 284
4X-RAY DIFFRACTION4A285 - 383
5X-RAY DIFFRACTION5B15 - 87
6X-RAY DIFFRACTION6B88 - 189
7X-RAY DIFFRACTION7B190 - 284
8X-RAY DIFFRACTION8B285 - 383
9X-RAY DIFFRACTION9C15 - 87
10X-RAY DIFFRACTION10C88 - 189
11X-RAY DIFFRACTION11C190 - 284
12X-RAY DIFFRACTION12C285 - 383
13X-RAY DIFFRACTION13D15 - 87
14X-RAY DIFFRACTION14D88 - 189
15X-RAY DIFFRACTION15D190 - 284
16X-RAY DIFFRACTION16D285 - 383

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