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- PDB-5zu2: Effect of mutation (R554A) on FAD modification in Aspergillus ory... -

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Basic information

Entry
Database: PDB / ID: 5zu2
TitleEffect of mutation (R554A) 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


choline dehydrogenase activity / glycine betaine biosynthetic process from choline / flavin adenine dinucleotide binding / mitochondrial inner membrane
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 / FLAVIN-ADENINE DINUCLEOTIDE / Glucose-methanol-choline oxidoreductase N-terminal domain-containing protein
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.441 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

Downloads & links

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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)195,69812
Polymers192,6923
Non-polymers3,0079
Water7,494416
1
A: formate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4306
Polymers64,2311
Non-polymers1,1995
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: formate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1343
Polymers64,2311
Non-polymers9042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: formate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1343
Polymers64,2311
Non-polymers9042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.320, 156.935, 184.601
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-837-

HOH

21A-885-

HOH

31C-786-

HOH

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Components

#1: Protein formate oxidase


Mass: 64230.637 Da / Num. of mol.: 3 / Mutation: R554A
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 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q2UD26
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-MPD / (4S)-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


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


Mass: 18.015 Da / Num. of mol.: 416 / 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 0.02 mm)
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 Msodium 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: BL41XU / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. obs: 81054 / % possible obs: 97.4 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 25.4
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 8070 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.441→38.83 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.63
RfactorNum. reflection% reflectionSelection details
Rfree0.2329 3928 4.87 %Random selection
Rwork0.1836 ---
obs0.186 80687 96.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.441→38.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13563 0 203 416 14182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914120
X-RAY DIFFRACTIONf_angle_d1.24619194
X-RAY DIFFRACTIONf_dihedral_angle_d8.2139447
X-RAY DIFFRACTIONf_chiral_restr0.0672064
X-RAY DIFFRACTIONf_plane_restr0.0072499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4411-2.47080.34471050.25632280X-RAY DIFFRACTION81
2.4708-2.50210.28541510.24552756X-RAY DIFFRACTION97
2.5021-2.5350.35751410.24482725X-RAY DIFFRACTION97
2.535-2.56980.31681240.24342753X-RAY DIFFRACTION97
2.5698-2.60650.28771190.23912756X-RAY DIFFRACTION98
2.6065-2.64540.28931570.23522740X-RAY DIFFRACTION98
2.6454-2.68670.26891260.22932784X-RAY DIFFRACTION97
2.6867-2.73070.31661440.23592704X-RAY DIFFRACTION97
2.7307-2.77780.29531590.23362735X-RAY DIFFRACTION98
2.7778-2.82830.30391390.22712791X-RAY DIFFRACTION97
2.8283-2.88270.26751300.2232737X-RAY DIFFRACTION97
2.8827-2.94150.31051470.2322735X-RAY DIFFRACTION97
2.9415-3.00540.3221460.23082730X-RAY DIFFRACTION97
3.0054-3.07530.28951400.21542768X-RAY DIFFRACTION97
3.0753-3.15220.30181490.21762739X-RAY DIFFRACTION97
3.1522-3.23740.25731310.21522776X-RAY DIFFRACTION97
3.2374-3.33260.26051390.20662719X-RAY DIFFRACTION97
3.3326-3.44010.25561500.19842769X-RAY DIFFRACTION97
3.4401-3.5630.21751330.18742754X-RAY DIFFRACTION97
3.563-3.70550.23781330.17652780X-RAY DIFFRACTION97
3.7055-3.8740.21351660.16862714X-RAY DIFFRACTION97
3.874-4.07810.17891230.16352799X-RAY DIFFRACTION97
4.0781-4.33320.2141520.15342733X-RAY DIFFRACTION97
4.3332-4.66730.18141540.13362779X-RAY DIFFRACTION97
4.6673-5.1360.16551300.14052798X-RAY DIFFRACTION97
5.136-5.8770.21521590.15562757X-RAY DIFFRACTION96
5.877-7.39610.1761400.14712817X-RAY DIFFRACTION96
7.3961-38.83490.13281410.11942831X-RAY DIFFRACTION94

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