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- PDB-6nes: FAD-dependent monooxygenase TropB from T. stipitatus -

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Basic information

Entry
Database: PDB / ID: 6nes
TitleFAD-dependent monooxygenase TropB from T. stipitatus
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 / HEXANE-1,6-DIOL / FAD-dependent monooxygenase tropB
Similarity search - Component
Biological speciesTalaromyces stipitatus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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)102,20912
Polymers99,8842
Non-polymers2,32510
Water8,665481
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7840 Å2
ΔGint-19 kcal/mol
Surface area34820 Å2
2
A: FAD-dependent monooxygenase tropB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0916
Polymers49,9421
Non-polymers1,1495
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: FAD-dependent monooxygenase tropB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1176
Polymers49,9421
Non-polymers1,1765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.805, 184.494, 164.129
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, 491 molecules

#2: Chemical
ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 481 / 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: 293.15 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: 1.75→46.43 Å / Num. obs: 107978 / % possible obs: 99.7 % / Redundancy: 12.8 % / Biso Wilson estimate: 34.02 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.027 / Rrim(I) all: 0.098 / Net I/σ(I): 1.11
Reflection shellResolution: 1.75→1.813 Å / Rmerge(I) obs: 1.952 / CC1/2: 0.602

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Cootmodel building
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EVY

5evy


Resolution: 1.75→46.43 Å / SU ML: 0.2288 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.4188
RfactorNum. reflection% reflection
Rfree0.1953 3862 1.85 %
Rwork0.1695 --
obs0.17 107896 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 44.15 Å2
Refinement stepCycle: LAST / Resolution: 1.75→46.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6760 0 154 481 7395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01047150
X-RAY DIFFRACTIONf_angle_d1.0819685
X-RAY DIFFRACTIONf_chiral_restr0.06031015
X-RAY DIFFRACTIONf_plane_restr0.00721252
X-RAY DIFFRACTIONf_dihedral_angle_d16.39214234
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.770.32291300.35156849X-RAY DIFFRACTION92.44
1.77-1.790.32881390.32347254X-RAY DIFFRACTION99.3
1.79-1.820.34661390.32117300X-RAY DIFFRACTION99.63
1.82-1.840.30261360.30327317X-RAY DIFFRACTION99.72
1.84-1.870.28471390.28917324X-RAY DIFFRACTION99.87
1.87-1.90.30521440.28657419X-RAY DIFFRACTION99.83
1.9-1.930.33251400.3357238X-RAY DIFFRACTION99.51
1.93-1.960.30611370.26287324X-RAY DIFFRACTION99.84
1.96-1.990.28281390.23297306X-RAY DIFFRACTION99.95
1.99-2.030.231380.23167343X-RAY DIFFRACTION99.93
2.03-2.070.27911380.2287318X-RAY DIFFRACTION99.97
2.07-2.110.25191360.227324X-RAY DIFFRACTION99.96
2.11-2.160.24661380.19727385X-RAY DIFFRACTION99.97
2.16-2.210.22981390.18787344X-RAY DIFFRACTION100
2.21-2.260.24651380.20867288X-RAY DIFFRACTION99.92
2.26-2.320.20411400.1877338X-RAY DIFFRACTION99.97
2.32-2.390.18491340.17177307X-RAY DIFFRACTION99.97
2.39-2.470.19291410.16547420X-RAY DIFFRACTION99.97
2.47-2.560.19361370.17257303X-RAY DIFFRACTION99.97
2.56-2.660.22051400.16827331X-RAY DIFFRACTION100
2.66-2.780.18541400.15697328X-RAY DIFFRACTION99.95
2.78-2.920.13551380.15337340X-RAY DIFFRACTION100
2.92-3.110.16871350.16047342X-RAY DIFFRACTION100
3.11-3.350.18931400.17547340X-RAY DIFFRACTION100
3.35-3.680.17461380.1547370X-RAY DIFFRACTION100
3.68-4.220.19721320.13517296X-RAY DIFFRACTION100
4.22-5.310.14061370.127337X-RAY DIFFRACTION100
5.31-47.070.17691400.1547368X-RAY DIFFRACTION99.85

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