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- PDB-3v3o: Crystal structure of TetX2 T280A: an adaptive mutant in complex w... -

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Basic information

Entry
Database: PDB / ID: 3v3o
TitleCrystal structure of TetX2 T280A: an adaptive mutant in complex with tigecycline
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 / TIGECYCLINE / Flavin-dependent monooxygenase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWalkiewicz, K. / Shamoo, Y.
CitationJournal: To be Published
Title: Crystal structure of TetX2 T280A: an adaptive mutant in complex with tigecycline
Authors: Walkiewicz, K. / Shamoo, Y.
History
DepositionDec 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)176,07818
Polymers170,0094
Non-polymers6,06914
Water41423
1
A: TetX2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0675
Polymers42,5021
Non-polymers1,5654
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TetX2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2607
Polymers42,5021
Non-polymers1,7576
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TetX2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8753
Polymers42,5021
Non-polymers1,3732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: TetX2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8753
Polymers42,5021
Non-polymers1,3732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.126, 80.080, 87.238
Angle α, β, γ (deg.)111.02, 89.97, 92.97
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 15:246 or resseq 251:377 )
21chain B and (resseq 15:246 or resseq 251:377 )
31chain C and (resseq 15:246 or resseq 251:377 )
41chain D and (resseq 15:246 or resseq 251:377 )

NCS domain segments:

Ens-ID: 1 / End auth comp-ID: LYS / End label comp-ID: LYS

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERchain 'A' and (resseq 15:246 or resseq 251:377 )AA15 - 2465 - 236
12VALVALchain 'A' and (resseq 15:246 or resseq 251:377 )AA251 - 377241 - 367
21SERSERchain 'B' and (resseq 15:246 or resseq 251:377 )BB15 - 2465 - 236
22VALVALchain 'B' and (resseq 15:246 or resseq 251:377 )BB251 - 377241 - 367
31SERSERchain 'C' and (resseq 15:246 or resseq 251:377 )CC15 - 2465 - 236
32VALVALchain 'C' and (resseq 15:246 or resseq 251:377 )CC251 - 377241 - 367
41SERSERchain 'D' and (resseq 15:246 or resseq 251:377 )DD15 - 2465 - 236
42VALVALchain 'D' and (resseq 15:246 or resseq 251:377 )DD251 - 377241 - 367

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Components

#1: Protein
TetX2 protein


Mass: 42502.141 Da / Num. of mol.: 4 / 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: 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
#4: Chemical
ChemComp-T1C / TIGECYCLINE / Tigecycline


Mass: 587.665 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C29H41N5O8 / Comment: medication, antibiotic*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.61 Å3/Da / Density % sol: 52.86 %
Crystal growTemperature: 283.15 K / Method: vapor diffusion, sitting drop / pH: 8.6
Details: Ammonium Sulfate, 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
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: 2.9→48.945 Å / Num. obs: 37001 / % possible obs: 96.74 % / Observed criterion σ(F): 0.06 / Redundancy: 1.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.9
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.9-2.96189.5
2.96-3.02194.4
3.02-3.08195.6
3.08-3.15197.3
3.15-3.23196.1
3.23-3.32197.3
3.32-3.42197.1
3.42-3.53197.7
3.53-3.65197.6
3.65-3.8197.4
3.8-3.97197.5
3.97-4.18197.7
4.18-4.44197.8
4.44-4.79197.8
4.79-5.27197.6
5.27-6.03198.1
6.03-7.59197.8
7.59-50197.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.1data extraction
JBluIce-EPICSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3P9U

3p9u


Resolution: 2.9→48.945 Å / Occupancy max: 1 / Occupancy min: 0.89 / SU ML: 0.44 / σ(F): 0.08 / Phase error: 34.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2975 1749 4.91 %
Rwork0.2317 --
obs0.2351 35593 93.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.8532 Å2-3.1327 Å21.9249 Å2
2--5.6776 Å27.1585 Å2
3----14.5308 Å2
Refinement stepCycle: LAST / Resolution: 2.9→48.945 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11513 0 410 23 11946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112181
X-RAY DIFFRACTIONf_angle_d1.54316550
X-RAY DIFFRACTIONf_dihedral_angle_d17.5044518
X-RAY DIFFRACTIONf_chiral_restr0.1131784
X-RAY DIFFRACTIONf_plane_restr0.0072133
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2814X-RAY DIFFRACTIONPOSITIONAL0.035
12B2814X-RAY DIFFRACTIONPOSITIONAL0.035
13C2814X-RAY DIFFRACTIONPOSITIONAL0.044
14D2818X-RAY DIFFRACTIONPOSITIONAL0.044
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.98530.3491250.26242429X-RAY DIFFRACTION80
2.9853-3.08170.32751410.26352699X-RAY DIFFRACTION89
3.0817-3.19180.3691320.26462723X-RAY DIFFRACTION92
3.1918-3.31960.37241560.25942848X-RAY DIFFRACTION94
3.3196-3.47060.35011480.24812878X-RAY DIFFRACTION95
3.4706-3.65350.32251430.23352850X-RAY DIFFRACTION95
3.6535-3.88240.29181480.23072821X-RAY DIFFRACTION94
3.8824-4.1820.29681450.22652891X-RAY DIFFRACTION95
4.182-4.60250.2841510.20962949X-RAY DIFFRACTION97
4.6025-5.26790.27121460.2142924X-RAY DIFFRACTION97
5.2679-6.63430.30211580.23722926X-RAY DIFFRACTION98
6.6343-48.95220.24361560.22312906X-RAY DIFFRACTION96

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