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- PDB-6a6r: Crystal structure of the modified fructosyl peptide oxidase from ... -

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Database: PDB / ID: 6a6r
TitleCrystal structure of the modified fructosyl peptide oxidase from Aspergillus nidulans, Seleno-methionine Derivative
ComponentsFructosyl amine: oxygen oxidoreductase
KeywordsOXIDOREDUCTASE / fructosyl peptide / oxidoreductase / Aspergillus nidulans / FAD-binding protein
Biological speciesAspergillus nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.609 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 29, 2018 / Release: May 15, 2019
RevisionDateData content typeProviderType
1.0May 15, 2019Structure modelrepositoryInitial release

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Deposited unit
A: Fructosyl amine: oxygen oxidoreductase
hetero molecules

Theoretical massNumber of molelcules
Total (without water)50,3305

TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-24 kcal/mol
Surface area18260 Å2
Unit cell
Length a, b, c (Å)73.199, 73.199, 162.305
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221


#1: Protein/peptide Fructosyl amine: oxygen oxidoreductase

Mass: 49143.629 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)

Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Flavin adenine dinucleotide / Comment: FAD *YM
#3: Chemical ChemComp-D1D / (4S,5S)-1,2-DITHIANE-4,5-DIOL

Mass: 152.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2S2
#4: Chemical ChemComp-SO4 / SULFATE ION

Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Sulfate
#5: Water ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O / Water

Experimental details


ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.84 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10.4
Details: 1.75 M ammonium sulfate, 0.2 M lithium sulfate, 0.08 M CAPS (N-cyclohexyl-3-aminopropanesulfonic acid) buffer (pH 10.4)

Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 15887 / % possible obs: 100 % / Redundancy: 20 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 44.3
Reflection shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 0.41 / % possible all: 100


HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.609→41.152 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.41
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.2558 766 4.82 %
Rwork0.2081 --
Obs0.2105 15887 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.609→41.152 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3381 0 74 46 3501
Refine LS restraints


TypeDev idealNumber
LS refinement shell


Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
Refinement TLS params.

Method: refined / Refinement-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)
Refinement TLS group


IDRefine TLS-IDSelection details
11chain 'A' and (resid 3 through 80 )
22chain 'A' and (resid 81 through 220 )
33chain 'A' and (resid 221 through 433 )

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