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- PDB-8blz: Engineered Fructosyl Peptide Oxidase - D02 mutant -

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Basic information

Entry
Database: PDB / ID: 8blz
TitleEngineered Fructosyl Peptide Oxidase - D02 mutant
ComponentsFructosyl Peptide Oxidase mutant (D02)
KeywordsOXIDOREDUCTASE / FAD / Deglycating enzyme / Amadori product / Fructosyl Peptide Oxidase
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE
Function and homology information
Biological speciesParastagonospora nodorum SN15 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsEstiri, H. / Bhattacharya, S. / Rodriguez-Buitrago, J.A. / Parisini, E.
Funding support1items
OrganizationGrant numberCountry
Other governmentlzp-2020/2-0013
CitationJournal: Sci Rep / Year: 2023
Title: Tailoring FPOX enzymes for enhanced stability and expanded substrate recognition.
Authors: Estiri, H. / Bhattacharya, S. / Buitrago, J.A.R. / Castagna, R. / Legzdina, L. / Casucci, G. / Ricci, A. / Parisini, E. / Gautieri, A.
History
DepositionNov 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Fructosyl Peptide Oxidase mutant (D02)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,67910
Polymers47,1481
Non-polymers1,5309
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-32 kcal/mol
Surface area17770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.096, 129.493, 86.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Fructosyl Peptide Oxidase mutant (D02)


Mass: 47148.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parastagonospora nodorum SN15 (fungus) / Gene: SNOG_08398 / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.71 Å3/Da / Density % sol: 54.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 20000 16-26%, MES 0.1M pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.7→64.75 Å / Num. obs: 55830 / % possible obs: 98.7 % / Redundancy: 12.7 % / CC1/2: 1 / Net I/σ(I): 12.6
Reflection shellResolution: 1.7→1.73 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2946 / CC1/2: 0.75

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y4J

6y4j


Resolution: 1.7→64.75 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.895 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19353 2729 4.9 %RANDOM
Rwork0.16769 ---
obs0.16896 53043 98.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.158 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.7→64.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3322 0 99 295 3716
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133540
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153277
X-RAY DIFFRACTIONr_angle_refined_deg1.7231.6424806
X-RAY DIFFRACTIONr_angle_other_deg1.4481.5867563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0655431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40522.044181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1515562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5421522
X-RAY DIFFRACTIONr_chiral_restr0.0870.2444
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023979
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02818
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_it1.9311.8211706
X-RAY DIFFRACTIONr_mcbond_other1.8771.821705
X-RAY DIFFRACTIONr_mcangle_it2.7712.7192131
X-RAY DIFFRACTIONr_mcangle_other2.7842.7222132
X-RAY DIFFRACTIONr_scbond_it3.1832.2611834
X-RAY DIFFRACTIONr_scbond_other3.1692.2611827
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8023.2012660
X-RAY DIFFRACTIONr_long_range_B_refined6.38521.9294047
X-RAY DIFFRACTIONr_long_range_B_other6.23921.633976
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 209 -
Rwork0.237 3879 -
obs--99.25 %

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