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- PDB-6a6s: Crystal structure of the modified fructosyl peptide oxidase from ... -

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Basic information

Entry
Database: PDB / ID: 6a6s
TitleCrystal structure of the modified fructosyl peptide oxidase from Aspergillus nidulans in complex with FSA, Seleno-methionine Derivative
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: 1.851 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 2.2Oct 30, 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)50,8729
Polymers49,1441
Non-polymers1,7298
Water3,621201
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-65 kcal/mol
Surface area17530 Å2
Unit cell
Length a, b, c (Å)72.753, 72.753, 159.687
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-789-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#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)
#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, 208 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.: 2 / Source method: obtained synthetically / Formula: C4H8O2S2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.48 Å3/Da / Density % sol: 50.45 %
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: BL44XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 42549 / % possible obs: 99.7 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 63.6
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.383 / Num. unique obs: 4077

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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: 1.851→35.468 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.65
RfactorNum. reflection% reflection
Rfree0.2235 1999 4.72 %
Rwork0.1908 --
obs0.1923 42387 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.851→35.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3381 0 105 201 3687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093584
X-RAY DIFFRACTIONf_angle_d1.2764862
X-RAY DIFFRACTIONf_dihedral_angle_d14.9731305
X-RAY DIFFRACTIONf_chiral_restr0.053514
X-RAY DIFFRACTIONf_plane_restr0.006609
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8506-1.89690.294990.25752750X-RAY DIFFRACTION96
1.8969-1.94820.28922030.23422786X-RAY DIFFRACTION100
1.9482-2.00550.26511040.23272897X-RAY DIFFRACTION100
2.0055-2.07020.3011980.22112808X-RAY DIFFRACTION100
2.0702-2.14420.26581030.21752883X-RAY DIFFRACTION100
2.1442-2.230.27451030.20872885X-RAY DIFFRACTION100
2.23-2.33150.29092010.2092817X-RAY DIFFRACTION100
2.3315-2.45440.246990.20782918X-RAY DIFFRACTION100
2.4544-2.60810.24021980.20782839X-RAY DIFFRACTION100
2.6081-2.80940.2576990.21282927X-RAY DIFFRACTION100
2.8094-3.0920.26531020.20872947X-RAY DIFFRACTION100
3.092-3.5390.22412010.19042867X-RAY DIFFRACTION100
3.539-4.45740.161970.15343020X-RAY DIFFRACTION100
4.4574-35.47440.16911920.16563044X-RAY DIFFRACTION99
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)
12.26130.765-0.65371.3829-0.40511.98330.18370.0080.17170.094-0.0316-0.0275-0.5221-0.2289-0.13430.32020.06830.00750.17470.00730.18832.7566-0.83323.0817
20.96810.4225-0.00190.7152-0.3962.3319-0.00680.03210.07670.09190.019-0.0026-0.3171-0.3055-0.01790.21970.097-0.00250.16970.01510.226530.3292-1.8343-8.6704
30.8681-0.0837-0.21921.03770.36853.9637-0.04240.0013-0.02660.0914-0.04170.2412-0.551-1.02210.09610.29190.23260.0570.43820.01460.299220.6167-2.225-7.4023
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 262 )
3X-RAY DIFFRACTION3chain 'A' and (resid 263 through 433 )

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