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- PDB-5mq6: Polycyclic Ketone Monooxygenase from the Thermophilic Fungus Ther... -

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Basic information

Entry
Database: PDB / ID: 5mq6
TitlePolycyclic Ketone Monooxygenase from the Thermophilic Fungus Thermothelomyces thermophila
ComponentsPyridine nucleotide-disulfide oxidoreductase-like protein
KeywordsOXIDOREDUCTASE / Flavin / monooxygenase / Baeyer-Villiger / oxygen / biocatalysis
Function / homology: / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily / oxidoreductase activity / nucleotide binding / FLAVIN-ADENINE DINUCLEOTIDE / Chem-NDP / Pyridine nucleotide-disulfide oxidoreductase-like protein
Function and homology information
Biological speciesMyceliophthora thermophila (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSavino, S. / Furst, M.J.L.J. / Fraaije, M.W. / Mattevi, A.
Funding support1items
OrganizationGrant numberCountry
EU-H2020635734
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Polycyclic Ketone Monooxygenase from the Thermophilic Fungus Thermothelomyces thermophila: A Structurally Distinct Biocatalyst for Bulky Substrates.
Authors: Furst, M.J. / Savino, S. / Dudek, H.M. / Gomez Castellanos, J.R. / Gutierrez de Souza, C. / Rovida, S. / Fraaije, M.W. / Mattevi, A.
History
DepositionDec 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Apr 22, 2020Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Jan 17, 2024Group: 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyridine nucleotide-disulfide oxidoreductase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8514
Polymers72,2281
Non-polymers1,6233
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-11 kcal/mol
Surface area24390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.200, 91.020, 133.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Pyridine nucleotide-disulfide oxidoreductase-like protein


Mass: 72228.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The organism is now called Thermothelomyces thermophila
Source: (gene. exp.) Myceliophthora thermophila (fungus) / Gene: MYCTH_65400 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G2QA95
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.49 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2.7 M ammonium sulfate, 100 mM MES sodium salt pH 6.5, and 5% v/v PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→75.21 Å / Num. obs: 49615 / % possible obs: 100 % / Redundancy: 6.2 % / CC1/2: 0.982 / Rmerge(I) obs: 0.162 / Net I/σ(I): 8.9
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.207 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YLT

2ylt


Resolution: 2→75.21 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.918 / SU B: 10.993 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R Free: 0.157 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23105 1541 3.1 %RANDOM
Rwork0.15269 ---
obs0.15515 48005 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.548 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å2-0 Å2-0 Å2
2---0.13 Å20 Å2
3---0.95 Å2
Refinement stepCycle: 1 / Resolution: 2→75.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4965 0 98 365 5428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0195204
X-RAY DIFFRACTIONr_bond_other_d0.0020.024835
X-RAY DIFFRACTIONr_angle_refined_deg2.1291.9767083
X-RAY DIFFRACTIONr_angle_other_deg2.106311148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0585636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0323.553228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.77915833
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7121536
X-RAY DIFFRACTIONr_chiral_restr0.1470.2753
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215841
X-RAY DIFFRACTIONr_gen_planes_other0.010.021190
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.5723.0252544
X-RAY DIFFRACTIONr_mcbond_other4.5583.0252543
X-RAY DIFFRACTIONr_mcangle_it5.2584.5213177
X-RAY DIFFRACTIONr_mcangle_other5.264.5213178
X-RAY DIFFRACTIONr_scbond_it4.7533.3922660
X-RAY DIFFRACTIONr_scbond_other4.7533.3922660
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2244.9233906
X-RAY DIFFRACTIONr_long_range_B_refined5.79436.756515
X-RAY DIFFRACTIONr_long_range_B_other5.72436.4096367
X-RAY DIFFRACTIONr_rigid_bond_restr6.759310039
X-RAY DIFFRACTIONr_sphericity_free24.6135113
X-RAY DIFFRACTIONr_sphericity_bonded10.267510155
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 103 -
Rwork0.266 3519 -
obs--100 %

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