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- PDB-7qfx: Crystal structure of Old Yellow Enzyme AnOYE8 from Aspergillus niger -

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Basic information

Entry
Database: PDB / ID: 7qfx
TitleCrystal structure of Old Yellow Enzyme AnOYE8 from Aspergillus niger
ComponentsNADH-dependent flavin oxidoreductase
KeywordsOXIDOREDUCTASE / Old Yellow Enzyme / Ene-reductase
Function / homologyNADPH dehydrogenase YqjM-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / NADPH dehydrogenase activity / FMN binding / NADP binding / Aldolase-type TIM barrel / FLAVIN MONONUCLEOTIDE / NADH-dependent flavin oxidoreductase
Function and homology information
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRobescu, M.S. / Loprete, G. / Vascon, F. / Gasparotto, M. / Filippini, F. / Bergantino, E. / Cendron, L.
Funding support1items
OrganizationGrant numberCountry
Other government
Citation
Journal: Int J Mol Sci / Year: 2022
Title: The Family Keeps on Growing: Four Novel Fungal OYEs Characterized.
Authors: Robescu, M.S. / Loprete, G. / Gasparotto, M. / Vascon, F. / Filippini, F. / Cendron, L. / Bergantino, E.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V.
History
DepositionDec 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: NADH-dependent flavin oxidoreductase
C: NADH-dependent flavin oxidoreductase
E: NADH-dependent flavin oxidoreductase
G: NADH-dependent flavin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,96813
Polymers183,6404
Non-polymers2,3289
Water1,53185
1
B: NADH-dependent flavin oxidoreductase
C: NADH-dependent flavin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9256
Polymers91,8202
Non-polymers1,1054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7950 Å2
ΔGint-79 kcal/mol
Surface area27170 Å2
MethodPISA
2
E: NADH-dependent flavin oxidoreductase
G: NADH-dependent flavin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,0437
Polymers91,8202
Non-polymers1,2235
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8210 Å2
ΔGint-89 kcal/mol
Surface area27500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.533, 65.388, 181.417
Angle α, β, γ (deg.)90.000, 107.760, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
NADH-dependent flavin oxidoreductase


Mass: 45910.000 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus niger (mold) / Gene: M747DRAFT_320366 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A370CG11
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.43 Å3/Da / Density % sol: 49.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 18 % w/v PEG 5000 MME, 0.1 M MES pH 6.5, 0.2 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.8→39.98 Å / Num. obs: 43316 / % possible obs: 97 % / Redundancy: 4.8 % / Biso Wilson estimate: 52.61 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.131 / Net I/σ(I): 13.2
Reflection shellResolution: 2.8→2.89 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 3 / Num. unique obs: 4327 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LNJ

5lnj


Resolution: 2.8→39.95 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2656 --RANDOM
Rwork0.2415 ---
obs-43315 95.99 %-
Displacement parametersBiso max: 151.91 Å2 / Biso mean: 72.6487 Å2 / Biso min: 30 Å2
Refinement stepCycle: LAST / Resolution: 2.8→39.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12554 0 152 85 12791

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