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- PDB-4wct: The crystal structure of Fructosyl amine: oxygen oxidoreductase (... -

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Basic information

Entry
Database: PDB / ID: 4wct
TitleThe crystal structure of Fructosyl amine: oxygen oxidoreductase (Amadoriase I) from Aspergillus fumigatus
ComponentsFructosyl amine:oxygen oxidoreductase
KeywordsOXIDOREDUCTASE / FAOX / FAODs
Function / homology
Function and homology information


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
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsRigoldi, F. / Gautieri, A. / Dalle Vedove, A. / Lucarelli, A.P. / Vesentini, S. / Parisini, E.
CitationJournal: Proteins / Year: 2016
Title: Crystal structure of the deglycating enzyme Amadoriase I in its free form and substrate-bound complex.
Authors: Rigoldi, F. / Gautieri, A. / Dalle Vedove, A. / Lucarelli, A.P. / Vesentini, S. / Parisini, E.
History
DepositionSep 5, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2May 25, 2016Group: Database references
Revision 1.3Jan 10, 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)104,2454
Polymers102,6742
Non-polymers1,5712
Water21,1141172
1
A: Fructosyl amine:oxygen oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1222
Polymers51,3371
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fructosyl amine:oxygen oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1222
Polymers51,3371
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.396, 83.100, 176.815
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 / Amadoriase 1


Mass: 51336.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (mold) / Plasmid: pET3a / Production host: Escherichia Coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: O42629
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1172 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Sodium citrate 0.1M, 10% PEG 4000, 15% 2-propanol / PH range: 5.6

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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: Jul 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.67→48.07 Å / Num. obs: 119826 / % possible obs: 98.85 % / Redundancy: 5.6 % / Net I/σ(I): 28.94
Reflection shellResolution: 1.67→1.76 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 3.4 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DJD

3djd


Resolution: 1.67→48.07 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.553 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16866 5993 5 %RANDOM
Rwork0.13936 ---
obs0.14083 113833 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.772 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å2-0 Å2
2---0.19 Å2-0 Å2
3----0.39 Å2
Refinement stepCycle: 1 / Resolution: 1.67→48.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6902 0 106 1172 8180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197330
X-RAY DIFFRACTIONr_bond_other_d00.026816
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.9649995
X-RAY DIFFRACTIONr_angle_other_deg0.684315769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0235916
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.68623.55338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.659151185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9971554
X-RAY DIFFRACTIONr_chiral_restr0.0920.21053
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.0218310
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021694
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_it1.9861.3433574
X-RAY DIFFRACTIONr_mcbond_other1.9811.3423573
X-RAY DIFFRACTIONr_mcangle_it2.70124478
X-RAY DIFFRACTIONr_mcangle_other2.7022.0024479
X-RAY DIFFRACTIONr_scbond_it3.5641.6783756
X-RAY DIFFRACTIONr_scbond_other3.5641.6773757
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2152.3675504
X-RAY DIFFRACTIONr_long_range_B_refined7.47613.3659715
X-RAY DIFFRACTIONr_long_range_B_other7.02111.9838899
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.668→1.712 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 411 -
Rwork0.211 7815 -
obs--93.01 %

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