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

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Basic information

Entry
Database: PDB / ID: 4a99
TitleSTRUCTURE OF THE TETRACYCLINE DEGRADING MONOOXYGENASE TETX IN COMPLEX WITH MINOCYCLINE
ComponentsTETX2 PROTEIN
KeywordsFLAVOPROTEIN / TETRACYCLINE DEGRADATION / MONOOXYGENASE / FLAVIN
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 / Chem-MIY / Flavin-dependent monooxygenase
Similarity search - Component
Biological speciesBACTEROIDES THETAIOTAOMICRON (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsVolkers, G. / Palm, G.J. / Weiss, M.S. / Hinrichs, W.
CitationJournal: 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
DepositionNov 25, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references / Structure summary
Revision 1.2Sep 11, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)186,57626
Polymers178,8144
Non-polymers7,76322
Water11,530640
1
A: TETX2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5005
Polymers44,7031
Non-polymers1,7974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TETX2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2356
Polymers44,7031
Non-polymers1,5315
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TETX2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6927
Polymers44,7031
Non-polymers1,9896
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: TETX2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1508
Polymers44,7031
Non-polymers2,4467
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
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 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: 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-IDAuth asym-IDLabel asym-ID
1AA - F
2BB - J
3CC - O
4DD - U

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

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Components

#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: 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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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 7 / Details: pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841
DetectorType: MARRESEARCH MAR165 / Detector: CCD / Date: Apr 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.18→80.94 Å / Num. obs: 86443 / % possible obs: 95.4 % / Observed criterion σ(I): 2 / Redundancy: 3.75 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.86
Reflection shellResolution: 2.18→2.31 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.37 / % possible all: 80.4

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Processing

Software
NameVersionClassification
REFMAC5.6.0116refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XDO

2xdo


Resolution: 2.18→80.94 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc 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.
RfactorNum. reflection% reflectionSelection details
Rfree0.23476 4301 5 %RANDOM
Rwork0.18462 ---
obs0.18713 82141 95.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 53.132 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20.31 Å20.03 Å2
2--0.99 Å21.27 Å2
3----1.11 Å2
Refinement stepCycle: LAST / Resolution: 2.18→80.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11496 0 526 640 12662
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212288
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9182.03216770
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15551462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.23525.624585
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.548151991
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0341552
X-RAY DIFFRACTIONr_chiral_restr0.1490.21837
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219340
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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 / Number: 2923 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.090.05
2Btight positional0.10.05
3Ctight positional0.070.05
4Dtight positional0.080.05
1Atight thermal3.790.5
2Btight thermal3.370.5
3Ctight thermal3.440.5
4Dtight thermal3.520.5
LS refinement shellResolution: 2.179→2.236 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 197 -
Rwork0.266 3857 -
obs--60.54 %
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)
11.17030.39140.80751.2534-0.13962.33740.0209-0.0441-0.0276-0.0290.0190.13060.0379-0.1967-0.03990.1078-0.0139-0.00290.11390.00730.1808-15.8467-0.868814.9502
21.18140.38390.50381.3401-0.07411.34590.05270.05330.0832-0.1663-0.01060.0349-0.0106-0.1149-0.04210.09780.010.00650.0925-0.01690.0904-11.03814.6579.8319
33.1315-0.0274-0.62622.6076-0.47112.70890.08520.21440.1119-0.179-0.0978-0.3485-0.01750.3450.01260.0738-0.00140.02050.168-0.0140.247813.61454.848215.1169
43.3257-0.10110.20742.4816-0.0721.3711-0.0085-0.14980.33250.160.03380.1413-0.2998-0.0349-0.02530.14480.05830.0080.0882-0.01990.1851-13.658216.319414.7415
51.5212-0.3864-0.66511.4733-0.61512.90480.02330.02710.02290.10070.03170.142-0.0492-0.1528-0.0550.1176-0.00860.00070.0939-0.00980.159413.835636.413740.8444
61.2565-0.3486-0.43591.3806-0.02441.48230.0733-0.0655-0.08730.2053-0.01070.02970.0697-0.0621-0.06260.1202-0.0109-0.0010.0947-0.00610.082318.60530.730946.0363
72.98840.08880.50182.2654-0.03622.36370.0848-0.2711-0.14380.2248-0.135-0.29890.06560.3510.05020.08610.0221-0.01010.21850.01080.250143.257630.436440.5855
83.36880.1175-0.31832.4943-0.3961.6924-0.00930.0921-0.3359-0.11630.00740.10660.359-0.08080.0020.1826-0.0744-0.01270.0896-0.02370.182815.9419.216440.8291
91.77060.22930.58281.61610.0591.9284-0.04790.0744-0.0808-0.0850.046-0.27840.00530.28870.00190.1879-0.06940.00140.1953-0.01730.1415-14.8768-23.556244.1826
101.76140.03560.47431.62060.03811.64140.0254-0.05340.00520.13630.0061-0.088-0.07970.208-0.03150.1725-0.0876-0.01010.14050.01950.068-19.5189-20.08351.1694
113.67470.5368-0.60073.27590.29793.4584-0.0939-0.27350.09020.1757-0.06680.322-0.1043-0.2210.16070.16750.015-0.00950.1545-0.01330.2441-44.2907-17.917646.3949
122.37010.44920.28422.32160.2681.26070.0519-0.08990.2190.0649-0.0792-0.0622-0.38270.14470.02730.2592-0.1212-0.01790.1569-0.02280.12-16.9498-7.343349.9869
131.7602-0.2316-0.83311.5751-0.24752.3449-0.0513-0.11880.10580.02420.0477-0.25240.07720.32730.00360.18330.05430.00290.1685-0.03310.15219.6207-22.126811.5224
141.9419-0.1299-0.35211.3849-0.01811.5968-0.02130.0424-0.0423-0.12910.0105-0.07870.11860.18730.01080.17610.05480.02370.09840.00250.071114.9725-25.59184.3266
153.8334-0.56350.37863.29220.09492.6634-0.07050.242-0.1887-0.15420.0120.28730.1529-0.21910.05860.1606-0.02020.01180.1506-0.01930.2467-9.8055-27.73659.3305
163.8941-0.3118-0.71122.04920.29841.038-0.04430.0346-0.3632-0.03540.0173-0.06980.40150.12520.02690.24790.08590.03280.1188-0.00960.130217.5262-38.3365.7023
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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