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- PDB-6a6v: Crystal structure of the modified fructosyl peptide oxidase from ... -

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Basic information

Entry
Database: PDB / ID: 6a6v
TitleCrystal structure of the modified fructosyl peptide oxidase from Aspergillus nidulans with 7 additional mutations, in complex with FSA
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 / FLAVIN-ADENINE DINUCLEOTIDE / 1-S-(carboxymethyl)-1-thio-beta-D-fructopyranose
Function and homology information
Biological speciesAspergillus nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_validate_close_contact / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.type / _pdbx_validate_close_contact.auth_atom_id_2
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fructosyl amine: oxygen oxidoreductase
H: Fructosyl amine: oxygen oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,0626
Polymers96,9832
Non-polymers2,0804
Water0
1
A: Fructosyl amine: oxygen oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5313
Polymers48,4911
Non-polymers1,0402
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: Fructosyl amine: oxygen oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5313
Polymers48,4911
Non-polymers1,0402
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.540, 135.540, 144.680
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Fructosyl amine: oxygen oxidoreductase


Mass: 48491.254 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#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.: 2 / Source method: obtained synthetically / Formula: C8H14O7S

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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: 3.96 Å3/Da / Density % sol: 68.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.8 / Details: 5% PGA, 20% PEG 3350, 0.1M CAPS (pH 8.8)

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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: 2.9→50 Å / Num. obs: 33508 / % possible obs: 99.9 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 14
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.852 / Num. unique obs: 3301

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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: 2.9→49.457 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.31
RfactorNum. reflection% reflection
Rfree0.2083 1597 4.78 %
Rwork0.1657 --
obs0.1678 33394 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→49.457 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6733 0 138 0 6871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077077
X-RAY DIFFRACTIONf_angle_d1.4779593
X-RAY DIFFRACTIONf_dihedral_angle_d12.2932567
X-RAY DIFFRACTIONf_chiral_restr0.1441018
X-RAY DIFFRACTIONf_plane_restr0.0051216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8997-2.99330.30921500.2482857X-RAY DIFFRACTION99
2.9933-3.10030.33491390.26112887X-RAY DIFFRACTION100
3.1003-3.22440.32521590.24282874X-RAY DIFFRACTION100
3.2244-3.37110.31711550.21872857X-RAY DIFFRACTION100
3.3711-3.54880.23311250.18992921X-RAY DIFFRACTION100
3.5488-3.77110.2141390.17832886X-RAY DIFFRACTION100
3.7711-4.06210.19951800.14882851X-RAY DIFFRACTION100
4.0621-4.47060.15111440.11862894X-RAY DIFFRACTION100
4.4706-5.1170.14251410.12072913X-RAY DIFFRACTION100
5.117-6.44460.18571140.14632933X-RAY DIFFRACTION100
6.4446-49.46450.15781510.14432924X-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)
13.77941.764-1.58184.6025-0.89122.6818-0.1177-0.0078-0.2267-0.0166-0.0378-0.47920.10430.44830.11230.2140.0492-0.01140.39740.03910.27113.9882-55.153-0.99
21.88480.9901-0.12943.559-1.04382.24420.0523-0.0726-0.00890.23650.0220.03970.13450.0101-0.0590.23550.11070.07290.2999-0.00190.23533.8521-57.12960.0502
31.998-0.2905-0.51982.1135-0.48532.4493-0.0738-0.12570.02060.31420.11860.0043-0.1119-0.1356-0.04830.24740.03410.03760.29830.02150.2967-1.7475-49.8730.0667
42.5597-0.8699-1.05463.18240.47272.3051-0.3090.5407-0.678-0.1529-0.26450.42490.319-0.72910.51710.4375-0.14090.10420.6346-0.24380.5023-7.8133-56.0381-46.9344
53.46530.1830.00152.51470.04472.2105-0.38270.3724-1.1747-0.2505-0.0149-0.53180.61890.11050.44270.6607-0.06530.30650.4867-0.21310.907415.3492-68.68-54.012
62.0321-0.2442-0.98741.64180.62642.2055-0.14420.4377-0.3759-0.4354-0.08760.0317-0.1531-0.26290.19530.4109-0.07670.05670.4458-0.14410.34411.8737-45.7423-48.7623
72.3629-0.0854-1.42631.02260.72593.4669-0.31490.1419-0.7174-0.2721-0.043-0.07560.1043-0.13660.34270.3716-0.08090.11430.3528-0.10610.4714.1027-51.0058-41.9631
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 234 )
3X-RAY DIFFRACTION3chain 'A' and (resid 235 through 434 )
4X-RAY DIFFRACTION4chain 'H' and (resid 3 through 80 )
5X-RAY DIFFRACTION5chain 'H' and (resid 81 through 160 )
6X-RAY DIFFRACTION6chain 'H' and (resid 161 through 332 )
7X-RAY DIFFRACTION7chain 'H' and (resid 333 through 434 )

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