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- PDB-5oc2: Crystal structure of Asp295Cys/Lys303Cys Amadoriase I mutant from... -

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Basic information

Entry
Database: PDB / ID: 5oc2
TitleCrystal structure of Asp295Cys/Lys303Cys 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 / oxidoreductase activity
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: 2.85 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

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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)104,1694
Polymers102,5982
Non-polymers1,5712
Water5,080282
1
A: Fructosyl amine:oxygen oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0842
Polymers51,2991
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fructosyl amine:oxygen oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0842
Polymers51,2991
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.853, 90.462, 81.307
Angle α, β, γ (deg.)90.00, 102.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fructosyl amine:oxygen oxidoreductase


Mass: 51298.766 Da / Num. of mol.: 2
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 / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.41 Å3/Da / Density % sol: 48.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate pH 5.6 14% Peg4K 5 % dimethyl sulfoxide

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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: May 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→48.82 Å / Num. obs: 22860 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.165 / Net I/av σ(I): 10.6 / Net I/σ(I): 10.59
Reflection shellResolution: 2.85→3 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 3316 / % possible all: 100

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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: 2.85→46.371 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.244 1150 5.04 %
Rwork0.1718 --
obs0.1756 22838 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→46.371 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6892 0 106 282 7280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087211
X-RAY DIFFRACTIONf_angle_d1.239807
X-RAY DIFFRACTIONf_dihedral_angle_d15.2992647
X-RAY DIFFRACTIONf_chiral_restr0.0761033
X-RAY DIFFRACTIONf_plane_restr0.0061278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8501-2.97980.28611570.18892669X-RAY DIFFRACTION100
2.9798-3.13680.30091320.1832719X-RAY DIFFRACTION100
3.1368-3.33330.26511310.17992691X-RAY DIFFRACTION100
3.3333-3.59060.251320.1712726X-RAY DIFFRACTION100
3.5906-3.95170.25941440.16062700X-RAY DIFFRACTION100
3.9517-4.52320.21441470.14882709X-RAY DIFFRACTION100
4.5232-5.69710.22091480.17012724X-RAY DIFFRACTION100
5.6971-46.37680.22461590.19352750X-RAY DIFFRACTION100

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