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- PDB-5oc3: Crystal structure of Ser67Cys/Pro121Cys Amadoriase I mutant from ... -

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Basic information

Entry
Database: PDB / ID: 5oc3
TitleCrystal structure of Ser67Cys/Pro121Cys Amadoriase I mutant from Aspergillus Fumigatus
ComponentsFructosyl amine:oxygen oxidoreductase
KeywordsOXIDOREDUCTASE / thermoresistance / flavin dependant enzyme / glycated aminoacid
Function / homology
Function and homology information


fructosyl-amino acid oxidase activity / saccharopine oxidase activity / sarcosine oxidase activity / flavin adenine dinucleotide binding
Similarity search - Function
MTOX family / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Fructosyl amine:oxygen oxidoreductase / Fructosyl amine:oxygen oxidoreductase
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.153 Å
AuthorsRigoldi, F. / Donini, S. / Gautieri, A. / Parisini, E.
Funding support Italy, 1items
OrganizationGrant numberCountry
Cariplo Foundation2013-0766 and 2016-0481 Italy
CitationJournal: Sci Rep / Year: 2018
Title: Thermal stabilization of the deglycating enzyme Amadoriase I by rational design.
Authors: Rigoldi, F. / Donini, S. / Giacomina, F. / Sorana, F. / Redaelli, A. / Bandiera, T. / Parisini, E. / Gautieri, A.
History
DepositionJun 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 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 1.2Nov 6, 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: Fructosyl amine:oxygen oxidoreductase
B: Fructosyl amine:oxygen oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,39416
Polymers102,7182
Non-polymers2,67614
Water16,628923
1
A: Fructosyl amine:oxygen oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7899
Polymers51,3591
Non-polymers1,4308
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fructosyl amine:oxygen oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6057
Polymers51,3591
Non-polymers1,2466
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.157, 83.081, 175.795
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 Fructosyl amine:oxygen oxidoreductase


Mass: 51358.844 Da / Num. of mol.: 2 / Mutation: S67C/P121C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (mold)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O42629, UniProt: Q4WIF5*PLUS
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 923 / 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: 50.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate pH 5.6 14% PEG4K 15 % isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1529→47.886 Å / Num. obs: 56549 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 15.95
Reflection shellResolution: 2.1529→2.27 Å / Redundancy: 7 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 6.3 / Num. unique obs: 8145 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4wct

4wct


Resolution: 2.153→47.886 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1807 2866 5.07 %
Rwork0.1392 --
obs0.1413 56474 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.153→47.886 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6900 0 178 923 8001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097310
X-RAY DIFFRACTIONf_angle_d1.1739923
X-RAY DIFFRACTIONf_dihedral_angle_d15.1292695
X-RAY DIFFRACTIONf_chiral_restr0.0771038
X-RAY DIFFRACTIONf_plane_restr0.0061286
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1529-2.190.2251350.14882640X-RAY DIFFRACTION99
2.19-2.22980.19251520.13992625X-RAY DIFFRACTION100
2.2298-2.27270.221380.14732656X-RAY DIFFRACTION100
2.2727-2.31910.18041440.13932621X-RAY DIFFRACTION100
2.3191-2.36960.22781390.14372676X-RAY DIFFRACTION100
2.3696-2.42470.2151460.152648X-RAY DIFFRACTION100
2.4247-2.48530.21071500.14772611X-RAY DIFFRACTION100
2.4853-2.55250.21081390.14232661X-RAY DIFFRACTION100
2.5525-2.62760.18241300.13712683X-RAY DIFFRACTION100
2.6276-2.71240.19721410.14032663X-RAY DIFFRACTION100
2.7124-2.80930.1961470.14642657X-RAY DIFFRACTION100
2.8093-2.92180.19511340.14462673X-RAY DIFFRACTION100
2.9218-3.05480.20631470.14622670X-RAY DIFFRACTION100
3.0548-3.21580.19251440.1382683X-RAY DIFFRACTION100
3.2158-3.41720.17851430.1272661X-RAY DIFFRACTION100
3.4172-3.6810.14291210.12862726X-RAY DIFFRACTION100
3.681-4.05120.15581560.11862689X-RAY DIFFRACTION100
4.0512-4.6370.13611680.11692708X-RAY DIFFRACTION100
4.637-5.84050.16511390.14632768X-RAY DIFFRACTION100
5.8405-47.89760.18131530.17412889X-RAY DIFFRACTION100

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