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- PDB-6a6u: Crystal structure of the modified fructosyl peptide oxidase from ... -

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Basic information

Entry
Database: PDB / ID: 6a6u
TitleCrystal structure of the modified fructosyl peptide oxidase from Aspergillus nidulans with R61G mutation, in complex with FSA
ComponentsFructosyl amine: oxygen oxidoreductase
KeywordsOXIDOREDUCTASE / fructosyl peptide / Aspergillus nidulans / FAD-binding protein
Function / homology
Function and homology information


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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
(4S,5S)-1,2-DITHIANE-4,5-DIOL / FLAVIN-ADENINE DINUCLEOTIDE / 1-S-(carboxymethyl)-1-thio-beta-D-fructopyranose
Similarity search - Component
Biological speciesAspergillus nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.945 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 2.0Jul 29, 2020Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)50,55810
Polymers48,6211
Non-polymers1,9379
Water5,098283
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-56 kcal/mol
Surface area17540 Å2
Unit cell
Length a, b, c (Å)72.922, 72.922, 160.053
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-860-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#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)
#3: Sugar ChemComp-FSA / 1-S-(carboxymethyl)-1-thio-beta-D-fructopyranose / 1-S-(carboxymethyl)-1-thio-beta-D-fructose / 1-S-(carboxymethyl)-1-thio-D-fructose / 1-S-(carboxymethyl)-1-thio-fructose


Type: D-saccharide, beta linking / Mass: 254.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H14O7S

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Non-polymers , 4 types, 291 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


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


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.53 Å3/Da / Density % sol: 51.32 %
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: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.945→50 Å / Num. obs: 36930 / % possible obs: 99.8 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 44.2
Reflection shellResolution: 1.95→1.98 Å / Rmerge(I) obs: 0.461 / Num. unique obs: 1828

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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

6a6r


Resolution: 1.945→40.755 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.86
RfactorNum. reflection% reflection
Rfree0.1982 1787 4.85 %
Rwork0.1738 --
obs0.175 36873 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.945→40.755 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3382 0 116 283 3781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013597
X-RAY DIFFRACTIONf_angle_d1.5834878
X-RAY DIFFRACTIONf_dihedral_angle_d13.9591315
X-RAY DIFFRACTIONf_chiral_restr0.202520
X-RAY DIFFRACTIONf_plane_restr0.006611
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9454-1.9980.23941390.19062549X-RAY DIFFRACTION96
1.998-2.05680.20851640.18042613X-RAY DIFFRACTION100
2.0568-2.12310.21440.17282685X-RAY DIFFRACTION100
2.1231-2.1990.21531470.16932648X-RAY DIFFRACTION100
2.199-2.28710.22271140.16592674X-RAY DIFFRACTION100
2.2871-2.39110.20641160.17212701X-RAY DIFFRACTION100
2.3911-2.51720.20281250.1762703X-RAY DIFFRACTION100
2.5172-2.67490.21061280.1822710X-RAY DIFFRACTION100
2.6749-2.88130.22441320.18172714X-RAY DIFFRACTION100
2.8813-3.17120.21651350.18732711X-RAY DIFFRACTION100
3.1712-3.62980.17221470.17132721X-RAY DIFFRACTION100
3.6298-4.57220.16851600.15312749X-RAY DIFFRACTION100
4.5722-40.76360.20231360.18122908X-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)
12.04710.6046-0.33191.70730.27210.90570.09140.00240.11260.0088-0.0127-0.0751-0.1859-0.0568-0.05940.1270.02570.00160.06320.00230.0932.8602-1.04253.387
20.84110.40880.36321.8099-0.4322.3807-0.09760.23460.1178-0.33720.05110.0812-0.05650.0840.04680.1431-0.00190.00760.16260.01510.169937.83582.6957-22.8562
31.4340.2341-0.55980.94450.11242.76070.0631-0.1783-0.00390.1816-0.05670.0783-0.1843-0.28290.0120.14230.00770.00850.1104-0.00260.103221.4789-3.678811.9794
40.6305-0.0116-0.12860.92530.60172.6841-0.01680.0409-0.02290.0149-0.05130.1406-0.1641-0.40660.06350.10030.05080.00920.12530.00830.140422.2804-3.5032-8.9107
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 160 )
3X-RAY DIFFRACTION3chain 'A' and (resid 161 through 234 )
4X-RAY DIFFRACTION4chain 'A' and (resid 235 through 434 )

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