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- PDB-6net: FAD-dependent monooxygenase TropB from T. stipitatus substrate complex -

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Basic information

Entry
Database: PDB / ID: 6net
TitleFAD-dependent monooxygenase TropB from T. stipitatus substrate complex
ComponentsFAD-dependent monooxygenase tropB
KeywordsFLAVOPROTEIN / oxidative dearomatization
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 / 2,4-dihydroxy-3,6-dimethylbenzaldehyde / FAD-dependent monooxygenase tropB
Similarity search - Component
Biological speciesTalaromyces stipitatus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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

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)102,11610
Polymers99,8842
Non-polymers2,2338
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint-37 kcal/mol
Surface area34250 Å2
2
A: FAD-dependent monooxygenase tropB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0955
Polymers49,9421
Non-polymers1,1534
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: FAD-dependent monooxygenase tropB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0215
Polymers49,9421
Non-polymers1,0794
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.405, 183.834, 164.234
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

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Protein , 1 types, 2 molecules AB

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


Mass: 49941.824 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 133 molecules

#2: Chemical ChemComp-KJY / 2,4-dihydroxy-3,6-dimethylbenzaldehyde


Mass: 166.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H10O3
#3: 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
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.78 Å3/Da / Density % sol: 55.81 %
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: 2.245→45.96 Å / Num. obs: 47286 / % possible obs: 99.8 % / Redundancy: 13.3 % / Biso Wilson estimate: 51.95 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.19 / Net I/σ(I): 1
Reflection shellResolution: 2.245→2.325 Å / Rmerge(I) obs: 2.457 / CC1/2: 0.41

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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: 2.25→45.96 Å / SU ML: 0.3754 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.2893
RfactorNum. reflection% reflection
Rfree0.2399 3845 3.92 %
Rwork0.1832 --
obs0.1855 47257 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 62.05 Å2
Refinement stepCycle: LAST / Resolution: 2.25→45.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6714 0 150 125 6989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01257165
X-RAY DIFFRACTIONf_angle_d1.19319732
X-RAY DIFFRACTIONf_chiral_restr0.05731013
X-RAY DIFFRACTIONf_plane_restr0.0081279
X-RAY DIFFRACTIONf_dihedral_angle_d15.4874162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.270.37071390.34753389X-RAY DIFFRACTION96.34
2.27-2.30.35191410.33053453X-RAY DIFFRACTION99.94
2.3-2.340.3361430.32193522X-RAY DIFFRACTION99.97
2.34-2.370.35821460.29853502X-RAY DIFFRACTION100
2.37-2.40.32571380.29063472X-RAY DIFFRACTION99.97
2.4-2.440.32061470.28683493X-RAY DIFFRACTION100
2.44-2.480.36151380.28983541X-RAY DIFFRACTION99.95
2.48-2.520.3381460.27663521X-RAY DIFFRACTION100
2.52-2.570.3521400.27833406X-RAY DIFFRACTION99.94
2.57-2.620.30451430.26813539X-RAY DIFFRACTION99.97
2.62-2.670.33811440.25833504X-RAY DIFFRACTION99.75
2.67-2.730.38981450.28643532X-RAY DIFFRACTION99.86
2.73-2.790.34131380.29463480X-RAY DIFFRACTION99.97
2.79-2.860.38021400.28233469X-RAY DIFFRACTION99.83
2.86-2.940.29541430.23193493X-RAY DIFFRACTION99.95
2.94-3.030.28561460.2063513X-RAY DIFFRACTION99.97
3.03-3.130.26661420.20533480X-RAY DIFFRACTION100
3.13-3.240.29711410.20573497X-RAY DIFFRACTION99.97
3.24-3.370.28511450.19613550X-RAY DIFFRACTION100
3.37-3.520.25291430.1733491X-RAY DIFFRACTION99.97
3.52-3.710.22711410.16013471X-RAY DIFFRACTION100
3.71-3.940.20021450.15213517X-RAY DIFFRACTION100
3.94-4.240.18471430.13553488X-RAY DIFFRACTION100
4.24-4.670.16581420.12233521X-RAY DIFFRACTION100
4.67-5.340.19961400.12423476X-RAY DIFFRACTION100
5.34-6.730.18271440.14483513X-RAY DIFFRACTION100
6.73-46.230.15151420.13643499X-RAY DIFFRACTION99.86

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