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- PDB-3djd: Crystal structure of the deglycating enzyme fructosamine oxidase ... -

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Basic information

Entry
Database: PDB / ID: 3djd
TitleCrystal structure of the deglycating enzyme fructosamine oxidase from Aspergillus fumigatus (Amadoriase II)
ComponentsFructosyl amine: oxygen oxidoreductase
KeywordsOXIDOREDUCTASE / fructosyl-amino acid / amadoriase / deglycation / fructosamine oxidase
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 speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsCollard, F. / Zhang, J. / Nemet, I. / Qanungo, K.R. / Monnier, V.M. / Yee, V.C.
CitationJournal: To be Published
Title: Crystal structure of the deglycating enzyme fructosamine oxidase (FAOX-II)
Authors: Collard, F. / Zhang, J. / Nemet, I. / Qanungo, K.R. / Monnier, V.M. / Yee, V.C.
History
DepositionJun 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)100,4304
Polymers98,8592
Non-polymers1,5712
Water15,169842
1
A: Fructosyl amine: oxygen oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2152
Polymers49,4301
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)50,2152
Polymers49,4301
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.310, 54.266, 106.252
Angle α, β, γ (deg.)90.00, 95.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fructosyl amine: oxygen oxidoreductase / fructosamine oxidase


Mass: 49429.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Production host: Escherichia coli (E. coli) / References: UniProt: P78573
#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.: 842 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsACCORDING TO THE AUTHORS THE SEQUENCE WAS VERIFIED BY SEQUENCING AND DIFFERS FROM THE UNP SEQUENCE ...ACCORDING TO THE AUTHORS THE SEQUENCE WAS VERIFIED BY SEQUENCING AND DIFFERS FROM THE UNP SEQUENCE P78573. IN THE DEPOSITED SEQUENCE RESIDUE 203 IS ALA.

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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: 2.16 Å3/Da / Density % sol: 42.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.1 M Hepes pH 7.4, 10 % iso-propanol, 18 % PEG 4000, protein solution 15 mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.75→36.96 Å / Num. obs: 85107 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.3 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 37.4
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 12 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 3.9 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→36.96 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.168 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20445 4254 5 %RANDOM
Rwork0.16734 ---
obs0.16921 80816 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.925 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.112 Å0.116 Å
Refinement stepCycle: LAST / Resolution: 1.75→36.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6678 0 106 842 7626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226966
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.9659473
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15850
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.37223.456327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.409151136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3161557
X-RAY DIFFRACTIONr_chiral_restr0.0980.21009
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025385
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.23518
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.24760
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2699
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.278
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.243
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0291.54342
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4426786
X-RAY DIFFRACTIONr_scbond_it2.24133058
X-RAY DIFFRACTIONr_scangle_it3.3844.52687
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 311 -
Rwork0.255 5806 -
obs--98.15 %

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