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- PDB-5zu3: Effect of mutation (R554K) on FAD modification in Aspergillus ory... -

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Basic information

Entry
Database: PDB / ID: 5zu3
TitleEffect of mutation (R554K) on FAD modification in Aspergillus oryzae RIB40formate oxidase
ComponentsFormate oxidase
KeywordsOXIDOREDUCTASE / Formate oxidase / 8-formyl-FAD / effect of mutation
Function / homology
Function and homology information


oxidoreductase activity, acting on CH-OH group of donors / flavin adenine dinucleotide binding
Similarity search - Function
Glucose Oxidase; domain 3 / Glucose Oxidase, domain 3 / GMC oxidoreductases signature 1. / Glucose-methanol-choline oxidoreductase / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain ...Glucose Oxidase; domain 3 / Glucose Oxidase, domain 3 / GMC oxidoreductases signature 1. / Glucose-methanol-choline oxidoreductase / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-FAY / Glucose-methanol-choline oxidoreductase N-terminal domain-containing protein
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsMikami, B. / Uchida, H. / Doubayashi, D.
Funding support Japan, 1items
OrganizationGrant numberCountry
16H04909 Japan
CitationJournal: J.Biochem. / Year: 2019
Title: The microenvironment surrounding FAD mediates its conversion to 8-formyl-FAD in Aspergillus oryzae RIB40 formate oxidase.
Authors: Doubayashi, D. / Oki, M. / Mikami, B. / Uchida, H.
History
DepositionMay 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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: Formate oxidase
B: Formate oxidase
C: Formate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,91512
Polymers192,8663
Non-polymers3,0499
Water9,764542
1
A: Formate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5026
Polymers64,2891
Non-polymers1,2135
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Formate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2063
Polymers64,2891
Non-polymers9182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Formate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2063
Polymers64,2891
Non-polymers9182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.462, 156.853, 184.947
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-870-

HOH

21A-921-

HOH

31A-927-

HOH

41A-933-

HOH

51A-935-

HOH

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Components

#1: Protein Formate oxidase


Mass: 64288.738 Da / Num. of mol.: 3 / Mutation: R554K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (strain ATCC 42149 / RIB 40) (mold)
Strain: ATCC 42149 / RIB 40 / Gene: AO090012000349 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2UD26
#2: Chemical ChemComp-FAY / [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-(8-formyl-7-methyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-2,3,4-trihydroxypentyl dihydrogen diphosphate / 8-FORMYL-FLAVIN-ADENINE DINUCLEOTIDE


Mass: 799.533 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H31N9O16P2
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 542 / Source method: isolated from a natural source / Formula: H2O

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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: 2.92 Å3/Da / Density % sol: 57.2 % / Description: rectangle plate (0.3 x 0.3 x 0.03)
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium acetate buffer pH 4.6, 6%(w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 84392 / % possible obs: 94.6 % / Redundancy: 6 % / Net I/σ(I): 28.7
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 5.6 / Num. unique obs: 4066 / % possible all: 92.6

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.4→38.866 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.27
RfactorNum. reflection% reflection
Rfree0.2561 4228 5.04 %
Rwork0.1947 --
obs0.1977 83865 93.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→38.866 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13575 0 206 542 14323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814143
X-RAY DIFFRACTIONf_angle_d1.16919221
X-RAY DIFFRACTIONf_dihedral_angle_d6.63710618
X-RAY DIFFRACTIONf_chiral_restr0.0642065
X-RAY DIFFRACTIONf_plane_restr0.0072498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3886-2.41580.35051270.27682321X-RAY DIFFRACTION82
2.4158-2.44420.32461320.27152572X-RAY DIFFRACTION92
2.4442-2.4740.35961570.26122528X-RAY DIFFRACTION91
2.474-2.50530.33511360.26112611X-RAY DIFFRACTION92
2.5053-2.53830.351360.26622568X-RAY DIFFRACTION92
2.5383-2.5730.3551320.25492621X-RAY DIFFRACTION93
2.573-2.60980.33281320.25942579X-RAY DIFFRACTION93
2.6098-2.64870.31221600.24912570X-RAY DIFFRACTION92
2.6487-2.69010.32461240.25982631X-RAY DIFFRACTION93
2.6901-2.73420.35541520.25042572X-RAY DIFFRACTION92
2.7342-2.78130.27581360.24032617X-RAY DIFFRACTION93
2.7813-2.83190.29711330.24622642X-RAY DIFFRACTION93
2.8319-2.88640.35031400.24582609X-RAY DIFFRACTION93
2.8864-2.94520.33471310.26252617X-RAY DIFFRACTION93
2.9452-3.00930.34751440.25522602X-RAY DIFFRACTION93
3.0093-3.07920.27891530.23522635X-RAY DIFFRACTION93
3.0792-3.15620.30381310.23752643X-RAY DIFFRACTION93
3.1562-3.24150.29611530.22382615X-RAY DIFFRACTION93
3.2415-3.33680.29951350.2262655X-RAY DIFFRACTION94
3.3368-3.44450.27721330.21332669X-RAY DIFFRACTION94
3.4445-3.56750.24921330.20382690X-RAY DIFFRACTION95
3.5675-3.71020.23191550.18782666X-RAY DIFFRACTION95
3.7102-3.8790.2121320.17192687X-RAY DIFFRACTION95
3.879-4.08330.22761490.16332681X-RAY DIFFRACTION94
4.0833-4.33880.19471270.15632732X-RAY DIFFRACTION95
4.3388-4.67330.1891250.13992772X-RAY DIFFRACTION96
4.6733-5.14260.2021380.14422801X-RAY DIFFRACTION97
5.1426-5.88450.21491540.15982839X-RAY DIFFRACTION99
5.8845-7.40550.20911740.15112899X-RAY DIFFRACTION100
7.4055-38.87060.17561640.12172993X-RAY DIFFRACTION100

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