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- PDB-6nev: FAD-dependent monooxygenase TropB from T. stipitatus Y239F Variant -

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Basic information

Entry
Database: PDB / ID: 6nev
TitleFAD-dependent monooxygenase TropB from T. stipitatus Y239F Variant
ComponentsFAD-dependent monooxygenase tropB
KeywordsFLAVOPROTEIN
Function / homology
Function and homology information


Oxidoreductases / secondary metabolite biosynthetic process / FAD binding / monooxygenase activity / membrane
Similarity search - Function
: / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FAD-dependent monooxygenase tropB
Similarity search - Component
Biological speciesTalaromyces stipitatus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.303 Å
AuthorsRodriguez Benitez, A. / Tweedy, S.E. / Baker Dockrey, S.A. / Lukowski, A.L. / Wymore, T. / Khare, D. / 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

Downloads & links

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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)101,4946
Polymers99,8522
Non-polymers1,6424
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-34 kcal/mol
Surface area35130 Å2
2
A: FAD-dependent monooxygenase tropB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7473
Polymers49,9261
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)50,7473
Polymers49,9261
Non-polymers8212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.259, 184.508, 163.257
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

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Components

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


Mass: 49925.824 Da / Num. of mol.: 2 / Mutation: Y239F
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


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.79 Å3/Da / Density % sol: 55.88 %
Crystal growTemperature: 293 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: 2.303→46.13 Å / Num. obs: 47286 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 52.99 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Net I/σ(I): 1.44
Reflection shellResolution: 2.303→2.386 Å / Rmerge(I) obs: 1.092 / CC1/2: 0.793

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Processing

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

6nes


Resolution: 2.303→46.13 Å / SU ML: 0.3514 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.1268
RfactorNum. reflection% reflection
Rfree0.233 3843 4.25 %
Rwork0.186 --
obs0.188 47257 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 63.12 Å2
Refinement stepCycle: LAST / Resolution: 2.303→46.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6769 0 108 118 6995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077120
X-RAY DIFFRACTIONf_angle_d0.8489661
X-RAY DIFFRACTIONf_chiral_restr0.05041014
X-RAY DIFFRACTIONf_plane_restr0.00511255
X-RAY DIFFRACTIONf_dihedral_angle_d16.60884207
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.39011380.35543142X-RAY DIFFRACTION97.07
2.33-2.360.37311420.34043211X-RAY DIFFRACTION99.94
2.36-2.40.32461430.31853186X-RAY DIFFRACTION99.91
2.4-2.430.35411390.30173201X-RAY DIFFRACTION99.76
2.43-2.470.34011450.29073280X-RAY DIFFRACTION99.85
2.47-2.50.33271410.29643191X-RAY DIFFRACTION99.79
2.5-2.550.31691430.28223184X-RAY DIFFRACTION99.94
2.55-2.590.30381470.27963245X-RAY DIFFRACTION99.76
2.59-2.640.34961330.25363159X-RAY DIFFRACTION99.97
2.64-2.690.35091460.23513245X-RAY DIFFRACTION99.71
2.69-2.740.2821420.22983183X-RAY DIFFRACTION99.94
2.74-2.80.27761430.23023227X-RAY DIFFRACTION99.94
2.8-2.870.31521420.22423201X-RAY DIFFRACTION99.85
2.87-2.940.25211420.2183251X-RAY DIFFRACTION99.97
2.94-3.020.28931410.21753183X-RAY DIFFRACTION99.94
3.02-3.110.30111440.21823209X-RAY DIFFRACTION100
3.11-3.210.26871440.21843238X-RAY DIFFRACTION100
3.21-3.320.25431410.2213195X-RAY DIFFRACTION99.85
3.32-3.450.2481400.19853195X-RAY DIFFRACTION99.85
3.45-3.610.2291470.18653220X-RAY DIFFRACTION99.85
3.61-3.80.24131430.18143225X-RAY DIFFRACTION99.91
3.8-4.040.21031460.16533202X-RAY DIFFRACTION99.94
4.04-4.350.19471420.14233216X-RAY DIFFRACTION99.88
4.35-4.790.15731450.13383195X-RAY DIFFRACTION99.97
4.79-5.480.19111420.14113253X-RAY DIFFRACTION99.97
5.48-6.90.21561430.16143194X-RAY DIFFRACTION99.94
6.9-46.140.16111390.13573220X-RAY DIFFRACTION99.64

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