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- PDB-3v3n: Crystal structure of TetX2 T280A: an adaptive mutant in complex w... -

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Basic information

Entry
Database: PDB / ID: 3v3n
TitleCrystal structure of TetX2 T280A: an adaptive mutant in complex with minocycline
ComponentsTetX2 protein
KeywordsOXIDOREDUCTASE/ANTIBIOTIC / Rossmann Fold / tetracycline degrading monooxygenase / OXIDOREDUCTASE-ANTIBIOTIC complex
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 / molecular replacement / Resolution: 2.703 Å
AuthorsWalkiewicz, K. / Shamoo, Y.
CitationJournal: To be Published
Title: Crystal structure of TetX2 T280A: an adaptive mutant in complex with minocycline
Authors: Walkiewicz, K. / Shamoo, Y.
History
DepositionDec 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / 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_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_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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)175,74920
Polymers170,0094
Non-polymers5,74116
Water2,702150
1
A: TetX2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9375
Polymers42,5021
Non-polymers1,4354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TetX2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9375
Polymers42,5021
Non-polymers1,4354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TetX2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9375
Polymers42,5021
Non-polymers1,4354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: TetX2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9375
Polymers42,5021
Non-polymers1,4354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.426, 80.102, 87.362
Angle α, β, γ (deg.)111.11, 90.10, 93.01
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 14:246 or resseq 250:382 )
21chain B and (resseq 14:246 or resseq 250:382 )
31chain C and (resseq 14:246 or resseq 250:382 )
41chain D and (resseq 14:246 or resseq 250:382 )

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEULYSLYSchain 'A' and (resseq 14:246 or resseq 250:382 )AA14 - 2464 - 236
12GLNGLNPHEPHEchain 'A' and (resseq 14:246 or resseq 250:382 )AA250 - 382240 - 372
21LEULEULYSLYSchain 'B' and (resseq 14:246 or resseq 250:382 )BB14 - 2464 - 236
22GLNGLNPHEPHEchain 'B' and (resseq 14:246 or resseq 250:382 )BB250 - 382240 - 372
31LEULEULYSLYSchain 'C' and (resseq 14:246 or resseq 250:382 )CC14 - 2464 - 236
32GLNGLNPHEPHEchain 'C' and (resseq 14:246 or resseq 250:382 )CC250 - 382240 - 372
41LEULEULYSLYSchain 'D' and (resseq 14:246 or resseq 250:382 )DD14 - 2464 - 236
42GLNGLNPHEPHEchain 'D' and (resseq 14:246 or resseq 250:382 )DD250 - 382240 - 372

NCS oper:
IDCodeMatrixVector
1given(-0.999155, 0.013139, -0.038949), (0.0001, -0.946756, -0.321951), (-0.041105, -0.321683, 0.945955)-38.838001, -18.172701, -3.82157
2given(-0.999446, -0.004031, 0.033027), (0.006816, 0.946773, 0.321829), (-0.032567, 0.321876, -0.946222)-8.49614, -58.584, -23.679399
3given(0.999993, -0.00194, -0.003083), (-0.00194, -0.999998, 0.00017), (-0.003083, -0.000164, -0.999995)34.214802, -35.099201, -7.09053

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Components

#1: Protein
TetX2 protein


Mass: 42502.141 Da / Num. of mol.: 4 / Fragment: TetX2 protein / Mutation: T280A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: Bacteroides thetaiotaomicron / Gene: tetX2 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: Q93L51
#2: 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 / Minocycline


Mass: 457.476 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H27N3O7 / Comment: medication, antibiotic*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.62 Å3/Da / Density % sol: 53.11 %
Crystal growTemperature: 283.15 K / Method: vapor diffusion, sitting drop / pH: 8.6
Details: Ammonium Sulafate, pH 8.6, VAPOR DIFFUSION, SITTING DROP, temperature 283.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00004 Å
DetectorType: NOIR-1 / Detector: CCD / Date: May 13, 2011
Details: Rosenbaum-Rock Si (111) sagitally focused monochromator
RadiationMonochromator: Rosenbaum-Rock Si (111) sagitally focused monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.703→50 Å / Num. obs: 43415 / % possible obs: 93 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.703-2.771.50.317184.7
2.77-2.821.60.302189.7
2.82-2.871.60.284192.2
2.87-2.931.60.233194.1
2.93-2.991.60.205192.6
2.99-3.061.60.175194.6
3.06-3.141.60.164192.4
3.14-3.221.60.137192.7
3.22-3.321.70.118192.5
3.32-3.431.70.113190.6
3.43-3.551.70.096192.5
3.55-3.691.70.092191.5
3.69-3.861.80.088193.3
3.86-4.061.80.083192.8
4.06-4.321.90.077192.7
4.32-4.651.90.066192.5
4.65-5.121.90.061195.5
5.12-5.861.90.061197
5.86-7.381.90.055198.2
7.38-501.90.048197.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.7 Å49.3 Å
Translation2.7 Å49.3 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
JBluIce-EPICSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3P9U

3p9u


Resolution: 2.703→49.297 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.87 / σ(F): 0.06 / Phase error: 30.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2757 1896 4.61 %RANDOM
Rwork0.2208 ---
obs0.2233 41120 87.01 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.317 Å2 / ksol: 0.321 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.5001 Å2-1.5437 Å2-0.0816 Å2
2--8.6507 Å29.3194 Å2
3----10.1508 Å2
Refinement stepCycle: LAST / Resolution: 2.703→49.297 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11559 0 384 150 12093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912199
X-RAY DIFFRACTIONf_angle_d1.23516573
X-RAY DIFFRACTIONf_dihedral_angle_d18.4184541
X-RAY DIFFRACTIONf_chiral_restr0.0791797
X-RAY DIFFRACTIONf_plane_restr0.0042145
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2874X-RAY DIFFRACTIONPOSITIONAL0.044
12B2874X-RAY DIFFRACTIONPOSITIONAL0.044
13C2874X-RAY DIFFRACTIONPOSITIONAL0.048
14D2874X-RAY DIFFRACTIONPOSITIONAL0.028
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.703-2.77060.4473950.33491844X-RAY DIFFRACTION58
2.7706-2.84550.39051080.30682552X-RAY DIFFRACTION78
2.8455-2.92920.35281370.28952594X-RAY DIFFRACTION82
2.9292-3.02370.38111330.27022710X-RAY DIFFRACTION85
3.0237-3.13180.28341350.25752870X-RAY DIFFRACTION88
3.1318-3.25720.32491340.23232877X-RAY DIFFRACTION89
3.2572-3.40540.27431450.22082869X-RAY DIFFRACTION90
3.4054-3.58490.28041430.21062873X-RAY DIFFRACTION90
3.5849-3.80940.25791490.20412946X-RAY DIFFRACTION90
3.8094-4.10340.2341370.19422903X-RAY DIFFRACTION91
4.1034-4.51610.22081390.17642930X-RAY DIFFRACTION91
4.5161-5.16890.21551390.1853011X-RAY DIFFRACTION94
5.1689-6.50990.28471510.21633114X-RAY DIFFRACTION97
6.5099-49.30510.27951510.23813131X-RAY DIFFRACTION97

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