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- PDB-7epw: Crystal structure of monooxygenase Tet(X4) with tigecycline -

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Basic information

Entry
Database: PDB / ID: 7epw
TitleCrystal structure of monooxygenase Tet(X4) with tigecycline
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 / TIGECYCLINE / Flavin-dependent monooxygenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 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 28, 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)44,7193
Polymers43,3441
Non-polymers1,3752
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-4 kcal/mol
Surface area17360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.400, 97.400, 168.980
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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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-T1C / TIGECYCLINE


Mass: 587.665 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H41N5O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 30% PEG4000, 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: 2.23→84.35 Å / Num. obs: 23785 / % possible obs: 99.6 % / Redundancy: 36.5 % / Rmerge(I) obs: 0.168 / Net I/σ(I): 22.5
Reflection shellResolution: 2.23→2.29 Å / Rmerge(I) obs: 1.917 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1715

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
XDS20200131data reduction
Aimless0.7.4data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EPV

7epv


Resolution: 2.23→48.7 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.131 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.243 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2389 2000 8.4 %RANDOM
Rwork0.1809 ---
obs0.1858 21708 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 138.17 Å2 / Biso mean: 47.528 Å2 / Biso min: 25.84 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 2.23→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2946 0 95 77 3118
Biso mean--58.39 43.88 -
Num. residues----373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133116
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172818
X-RAY DIFFRACTIONr_angle_refined_deg1.581.6654232
X-RAY DIFFRACTIONr_angle_other_deg1.2881.5956572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0845373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.56924.337166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.3615537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3031514
X-RAY DIFFRACTIONr_chiral_restr0.0710.2401
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023468
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02607
LS refinement shellResolution: 2.23→2.288 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 144 -
Rwork0.248 1567 -
all-1711 -
obs--100 %

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