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

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Basic information

Entry
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 / 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 / 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.
History
DepositionJun 29, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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)50,3305
Polymers49,1441
Non-polymers1,1864
Water82946
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
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

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Components

#1: Protein 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)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / 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
#5: Water ChemComp-HOH / water


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

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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: 2.55 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)

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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

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
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
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033555
X-RAY DIFFRACTIONf_angle_d1.1194823
X-RAY DIFFRACTIONf_dihedral_angle_d11.9971295
X-RAY DIFFRACTIONf_chiral_restr0.035513
X-RAY DIFFRACTIONf_plane_restr0.004609
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6088-2.81020.32861470.24822908X-RAY DIFFRACTION97
2.8102-3.09290.31331460.25092971X-RAY DIFFRACTION100
3.0929-3.54030.25931360.22093023X-RAY DIFFRACTION100
3.5403-4.45950.22451550.18083042X-RAY DIFFRACTION100
4.4595-41.15730.24421820.19793177X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.8292-0.68240.05921.13260.571.42410.10180.0191-0.0118-0.03510.0881-0.1397-0.14180.1058-0.17440.2143-0.0462-0.01710.2572-0.00170.217515.7715-28.954530.1891
21.1156-0.2125-0.67991.08960.04372.26920.00740.04990.0508-0.09780.0256-0.1282-0.00330.0769-0.03810.16540.0028-0.02710.2330.02590.264315.6387-27.99319.1268
31.0748-0.03610.59320.90050.58772.7995-0.0109-0.03510.1609-0.0189-0.09740.0962-0.5101-0.03930.11170.3414-0.03610.04570.2143-0.00880.31818.1812-20.250318.6668
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 80 )
2X-RAY DIFFRACTION2chain 'A' and (resid 81 through 220 )
3X-RAY DIFFRACTION3chain 'A' and (resid 221 through 433 )

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