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- PDB-7epv: Crystal structure of tigecycline degrading monooxygenase Tet(X4) -

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Basic information

Entry
Database: PDB / ID: 7epv
TitleCrystal structure of tigecycline degrading monooxygenase Tet(X4)
ComponentsFlavin-dependent monooxygenase
KeywordsOXIDOREDUCTASE / monooxygenase / Tet(X4) / tigecycline resistance
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor / 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 superfamily
Similarity search - Domain/homology
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / Flavin-dependent monooxygenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsCheng, Q. / Chen, S.
CitationJournal: Bmc Biol. / Year: 2021
Title: Structural and mechanistic basis of the high catalytic activity of monooxygenase Tet(X4) on tigecycline.
Authors: Cheng, Q. / Cheung, Y. / Liu, C. / Xiao, Q. / Sun, B. / Zhou, J. / Chan, E.W.C. / Zhang, R. / Chen, S.
History
DepositionApr 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 16, 2022Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flavin-dependent monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4085
Polymers43,3441
Non-polymers1,0644
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-1 kcal/mol
Surface area17310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.530, 97.530, 168.530
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-561-

HOH

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Components

#1: Protein Flavin-dependent monooxygenase / TetX monooxygenase / TetX


Mass: 43343.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tet(X)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A3T0V9Y5, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of ...References: UniProt: A0A3T0V9Y5, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor
#2: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H35N9O15P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.67 Å3/Da / Density % sol: 53.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: PEG 4000, 0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6
PH range: 5.4-5.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.78→27.77 Å / Num. obs: 46095 / % possible obs: 100 % / Redundancy: 33.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 29.4
Reflection shellResolution: 1.78→1.83 Å / Rmerge(I) obs: 1.335 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3306 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XDO

2xdo


Resolution: 1.78→27.74 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.227 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1983 2156 4.9 %RANDOM
Rwork0.1654 ---
obs0.1671 41959 95.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.01 Å2 / Biso mean: 23.06 Å2 / Biso min: 9.09 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.78→27.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2914 0 71 244 3229
Biso mean--21.69 32.42 -
Num. residues----369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133087
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172805
X-RAY DIFFRACTIONr_angle_refined_deg1.7251.6414173
X-RAY DIFFRACTIONr_angle_other_deg1.4971.5786546
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6195372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68824.303165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12715535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9041514
X-RAY DIFFRACTIONr_chiral_restr0.090.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023429
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02602
LS refinement shellResolution: 1.78→1.826 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 128 -
Rwork0.229 2755 -
all-2883 -
obs--87.36 %

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