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- PDB-6a6t: Crystal structure of the modified fructosyl peptide oxidase from ... -

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Basic information

Entry
Database: PDB / ID: 6a6t
TitleCrystal structure of the modified fructosyl peptide oxidase from Aspergillus nidulans with R61G mutation
ComponentsFructosyl amine: oxygen oxidoreductase
KeywordsOXIDOREDUCTASE / fructosyl peptide / Aspergillus nidulans / FAD-binding protein
Function / homologyD-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 / 2-Layer Sandwich / Alpha Beta / (4S,5S)-1,2-DITHIANE-4,5-DIOL / FLAVIN-ADENINE DINUCLEOTIDE
Function and homology information
Biological speciesAspergillus nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsOgawa, N. / Maruyama, Y. / Itoh, T. / Hashimoto, W. / Murata, K.
CitationJournal: Sci Rep / Year: 2019
Title: Creation of haemoglobin A1c direct oxidase from fructosyl peptide oxidase by combined structure-based site specific mutagenesis and random mutagenesis.
Authors: Ogawa, N. / Kimura, T. / Umehara, F. / Katayama, Y. / Nagai, G. / Suzuki, K. / Aisaka, K. / Maruyama, Y. / Itoh, T. / Hashimoto, W. / Murata, K. / Ichimura, M.
History
DepositionJun 29, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,55211
Polymers48,6211
Non-polymers1,93110
Water2,864159
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-67 kcal/mol
Surface area17300 Å2
Unit cell
Length a, b, c (Å)72.349, 72.349, 160.114
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Fructosyl amine: oxygen oxidoreductase


Mass: 48621.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus nidulans (mold) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-D1D / (4S,5S)-1,2-DITHIANE-4,5-DIOL


Mass: 152.235 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H8O2S2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.49 Å3/Da / Density % sol: 50.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10.4
Details: 1.75 M ammonium sulfate, 0.2 M lithium sulfate, and 0.08 M CAPS (N-cyclohexyl-3-aminopropanesulfonic acid) buffer (pH 10.4)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 38889 / % possible obs: 99.6 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 14.1
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.405 / Num. unique obs: 1893

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A6R
Resolution: 1.901→33.732 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.76
RfactorNum. reflection% reflection
Rfree0.2635 1828 4.72 %
Rwork0.2299 --
obs0.2315 38699 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.901→33.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3367 0 113 159 3639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073575
X-RAY DIFFRACTIONf_angle_d1.424849
X-RAY DIFFRACTIONf_dihedral_angle_d13.4251304
X-RAY DIFFRACTIONf_chiral_restr0.059516
X-RAY DIFFRACTIONf_plane_restr0.006607
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9013-1.95280.38561360.32822790X-RAY DIFFRACTION99
1.9528-2.01020.35851310.33752800X-RAY DIFFRACTION99
2.0102-2.07510.40441680.31042773X-RAY DIFFRACTION99
2.0751-2.14920.35281400.2822781X-RAY DIFFRACTION100
2.1492-2.23530.34621430.282815X-RAY DIFFRACTION99
2.2353-2.3370.34051250.27332822X-RAY DIFFRACTION99
2.337-2.46020.27561390.26662804X-RAY DIFFRACTION99
2.4602-2.61420.30211410.25662832X-RAY DIFFRACTION99
2.6142-2.8160.29271360.25412816X-RAY DIFFRACTION99
2.816-3.09920.30351580.24962844X-RAY DIFFRACTION100
3.0992-3.54720.23111170.21682901X-RAY DIFFRACTION100
3.5472-4.46750.20261560.17532838X-RAY DIFFRACTION98
4.4675-33.73760.18971380.19063055X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.5350.97780.77051.64080.40670.64230.24930.2686-0.16630.1674-0.03240.05120.54940.3772-0.18170.45470.14530.00390.2617-0.01230.2087-32.52331.1023.1637
20.53210.3315-0.06490.91410.78012.13530.00350.0183-0.10820.18570.0917-0.03860.31180.3102-0.0840.30420.14090.01620.2571-0.01330.2303-29.96020.2178-6.6845
30.65080.1110.72151.13220.01612.9937-0.03670.18480.02980.18970.0892-0.17450.37181.08960.02780.32210.2746-0.05330.5728-0.04270.296-22.00723.3637-8.9067
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 80 )
2X-RAY DIFFRACTION2chain 'A' and (resid 81 through 234 )
3X-RAY DIFFRACTION3chain 'A' and (resid 235 through 433 )

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