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- PDB-6neu: FAD-dependent monooxygenase TropB from T. stipitatus R206Q variant -

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Basic information

Entry
Database: PDB / ID: 6neu
TitleFAD-dependent monooxygenase TropB from T. stipitatus R206Q variant
ComponentsFAD-dependent monooxygenase tropB
KeywordsFLAVOPROTEIN / oxidative dearomatization
Function / homologyFAD-binding domain / FAD binding domain / Oxidoreductases / FAD binding / monooxygenase activity / FAD/NAD(P)-binding domain superfamily / membrane / FLAVIN-ADENINE DINUCLEOTIDE / FAD-dependent monooxygenase tropB
Function and homology information
Biological speciesTalaromyces stipitatus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRodriguez Benitez, A. / Tweedy, S.E. / Baker Dockrey, S.A. / Lukowski, A.L. / Wymore, T. / Khare, D. / Brooks, C.L. / Palfey, B.A. / Smith, J.L. / Narayan, A.R.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124880 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK042303 United States
CitationJournal: Acs Catalysis / Year: 2019
Title: Structural basis for selectivity in flavin-dependent monooxygenase-catalyzed oxidative dearomatization.
Authors: Rodriguez Benitez, A. / Tweedy, S.E. / Baker Dockrey, S.A. / Lukowski, A.L. / Wymore, T. / Khare, D. / Brooks 3rd, C.L. / Palfey, B.A. / Smith, J.L. / Narayan, A.R.H.
History
DepositionDec 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FAD-dependent monooxygenase tropB
B: FAD-dependent monooxygenase tropB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,5607
Polymers99,8262
Non-polymers1,7345
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-34 kcal/mol
Surface area35480 Å2
2
A: FAD-dependent monooxygenase tropB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7343
Polymers49,9131
Non-polymers8212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: FAD-dependent monooxygenase tropB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8264
Polymers49,9131
Non-polymers9133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.801, 184.173, 163.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-680-

HOH

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Components

#1: Protein FAD-dependent monooxygenase tropB / Tropolone synthesis protein B


Mass: 49912.758 Da / Num. of mol.: 2 / Mutation: R206Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Talaromyces stipitatus (strain ATCC 10500 / CBS 375.48 / QM 6759 / NRRL 1006) (fungus)
Strain: ATCC 10500 / CBS 375.48 / QM 6759 / NRRL 1006 / Gene: tropB, tsL1, TSTA_117740 / Production host: Escherichia coli (E. coli) / References: UniProt: B8M9J8
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.77 Å3/Da / Density % sol: 55.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: 1.11 M ammonium tartrate dibasic, 6% hexanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.3→46.91 Å / Num. obs: 47799 / % possible obs: 99.7 % / Redundancy: 12.9 % / Biso Wilson estimate: 50.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.192 / Net I/σ(I): 1.45
Reflection shellResolution: 2.3→2.382 Å / Rmerge(I) obs: 1.48 / CC1/2: 0.735

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Coot1.14_3260model building
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NES

6nes


Resolution: 2.3→46.91 Å / SU ML: 0.4012 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.5219
RfactorNum. reflection% reflection
Rfree0.2508 3825 4.18 %
Rwork0.1906 --
obs0.1931 47766 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 58.93 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6767 0 114 137 7018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127127
X-RAY DIFFRACTIONf_angle_d1.21219673
X-RAY DIFFRACTIONf_chiral_restr0.05731015
X-RAY DIFFRACTIONf_plane_restr0.00781256
X-RAY DIFFRACTIONf_dihedral_angle_d16.50984212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.35191290.32573032X-RAY DIFFRACTION94.05
2.33-2.360.40721460.3373301X-RAY DIFFRACTION100
2.36-2.390.37551420.32093229X-RAY DIFFRACTION99.94
2.39-2.430.34991400.33173283X-RAY DIFFRACTION99.88
2.43-2.460.43881430.31323245X-RAY DIFFRACTION99.88
2.46-2.50.31941400.31153193X-RAY DIFFRACTION99.82
2.5-2.540.30041460.2823323X-RAY DIFFRACTION99.83
2.54-2.590.36791370.29043223X-RAY DIFFRACTION99.7
2.59-2.630.36391440.25643260X-RAY DIFFRACTION99.94
2.63-2.680.29851400.23463211X-RAY DIFFRACTION99.64
2.68-2.740.25051450.22653308X-RAY DIFFRACTION99.74
2.74-2.80.31440.25533200X-RAY DIFFRACTION99.91
2.8-2.860.33771420.25633255X-RAY DIFFRACTION99.85
2.86-2.930.30761460.25513286X-RAY DIFFRACTION99.91
2.93-3.010.41361400.23733223X-RAY DIFFRACTION99.91
3.01-3.10.34731410.26723254X-RAY DIFFRACTION99.88
3.1-3.20.40891420.25423258X-RAY DIFFRACTION100
3.2-3.320.29371450.22623249X-RAY DIFFRACTION99.94
3.32-3.450.24111420.19163242X-RAY DIFFRACTION99.97
3.45-3.610.24171400.1743286X-RAY DIFFRACTION100
3.61-3.80.23441440.1763283X-RAY DIFFRACTION100
3.8-4.030.23911380.15033217X-RAY DIFFRACTION100
4.03-4.350.20531460.12843266X-RAY DIFFRACTION100
4.35-4.780.16131430.13153243X-RAY DIFFRACTION100
4.78-5.470.19381410.143300X-RAY DIFFRACTION100
5.47-6.890.19761340.15533239X-RAY DIFFRACTION99.97
6.89-46.920.1611450.13573269X-RAY DIFFRACTION99.91

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