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- PDB-7blf: Crystal structure of ene-reductase OYE4 from Botryotinia fuckelia... -

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Basic information

Entry
Database: PDB / ID: 7blf
TitleCrystal structure of ene-reductase OYE4 from Botryotinia fuckeliana (BfOYE4)
ComponentsOxidored_FMN domain-containing protein
KeywordsOXIDOREDUCTASE / NADPH dehydrogenase
Function / homology
Function and homology information


NADPH dehydrogenase activity / FMN binding / NADP binding
Similarity search - Function
NADPH dehydrogenase YqjM-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / FORMIC ACID / NADH:flavin oxidoreductase/NADH oxidase N-terminal domain-containing protein
Similarity search - Component
Biological speciesBotryotinia fuckeliana (gray fruit mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsRobescu, M.S. / Bergantino, E. / Hall, M. / Cendron, L.
CitationJournal: Acs Catalysis / Year: 2022
Title: Asymmetric Proton Transfer Catalysis by Stereocomplementary Old Yellow Enzymes for C=C Bond Isomerization Reaction
Authors: Robescu, M.S. / Cendron, L. / Bacchin, A. / Wagner, K. / Reiter, T. / Janicki, I. / Merusic, K. / Illek, M. / Aleotti, M. / Bergantino, E. / Hall, M.
History
DepositionJan 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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
A: Oxidored_FMN domain-containing protein
B: Oxidored_FMN domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1976
Polymers99,1922
Non-polymers1,0054
Water8,251458
1
A: Oxidored_FMN domain-containing protein
hetero molecules

A: Oxidored_FMN domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1976
Polymers99,1922
Non-polymers1,0054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area6620 Å2
ΔGint-34 kcal/mol
Surface area28550 Å2
MethodPISA
2
B: Oxidored_FMN domain-containing protein
hetero molecules

B: Oxidored_FMN domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1976
Polymers99,1922
Non-polymers1,0054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area6360 Å2
ΔGint-37 kcal/mol
Surface area28140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.040, 92.061, 161.998
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Oxidored_FMN domain-containing protein / NADPH dehydrogenase / OYE4


Mass: 49596.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Botryotinia fuckeliana (strain B05.10) (fungus)
Strain: B05.10 / Gene: BCIN_13g05380 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A384K246
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 2.33 Å3/Da / Density % sol: 47.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM Na-HEPES, 28% v/v PEG 400 and 200 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.15→92.07 Å / Num. obs: 96306 / % possible obs: 99.47 % / Redundancy: 5.4 % / Biso Wilson estimate: 29.02 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.117 / Net I/σ(I): 9.4 / Num. measured all: 275861
Reflection shellResolution: 2.15→2.227 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.748 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 22734 / CC1/2: 0.617

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5nux

5nux


Resolution: 2.15→49.03 Å / SU ML: 0.2414 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.1742
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2185 4772 4.96 %
Rwork0.1811 91534 -
obs0.1829 96306 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.27 Å2
Refinement stepCycle: LAST / Resolution: 2.15→49.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6237 0 68 460 6765
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00886486
X-RAY DIFFRACTIONf_angle_d1.14198801
X-RAY DIFFRACTIONf_chiral_restr0.181948
X-RAY DIFFRACTIONf_plane_restr0.00631131
X-RAY DIFFRACTIONf_dihedral_angle_d25.11172380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.170.28521850.28493025X-RAY DIFFRACTION99.2
2.17-2.20.34381430.28983073X-RAY DIFFRACTION98.14
2.2-2.230.2851690.29353028X-RAY DIFFRACTION98.73
2.23-2.260.29611570.2843053X-RAY DIFFRACTION99.26
2.26-2.280.30571810.27473070X-RAY DIFFRACTION99.54
2.28-2.320.29741370.26063113X-RAY DIFFRACTION99.72
2.32-2.350.28321510.24033070X-RAY DIFFRACTION99.75
2.35-2.380.231630.23963095X-RAY DIFFRACTION99.54
2.38-2.420.31341340.22693119X-RAY DIFFRACTION99.6
2.42-2.460.29511630.22423074X-RAY DIFFRACTION99.75
2.46-2.50.25891410.20723062X-RAY DIFFRACTION99.56
2.5-2.550.31011500.20193114X-RAY DIFFRACTION99.66
2.55-2.60.24641650.19723032X-RAY DIFFRACTION99.66
2.6-2.650.23841800.19553088X-RAY DIFFRACTION99.6
2.65-2.710.25772120.18663023X-RAY DIFFRACTION99.14
2.71-2.770.22161520.19153055X-RAY DIFFRACTION99.13
2.77-2.840.26011510.18493065X-RAY DIFFRACTION98.59
2.84-2.920.27221490.19283053X-RAY DIFFRACTION98.77
2.92-30.26421640.19673034X-RAY DIFFRACTION99.29
3-3.10.2131610.18963099X-RAY DIFFRACTION99.3
3.1-3.210.20321530.18663036X-RAY DIFFRACTION99.07
3.21-3.340.23061420.17843080X-RAY DIFFRACTION99.11
3.34-3.490.19991600.17143046X-RAY DIFFRACTION98.65
3.49-3.680.21450.16183068X-RAY DIFFRACTION98.08
3.68-3.910.17591530.15973004X-RAY DIFFRACTION97.83
3.91-4.210.15271510.14112995X-RAY DIFFRACTION96.5
4.21-4.630.17951710.12712994X-RAY DIFFRACTION97.26
4.63-5.30.16271720.13142989X-RAY DIFFRACTION97.5
5.3-6.670.19471520.15033004X-RAY DIFFRACTION97.2
6.68-49.030.15491650.13892973X-RAY DIFFRACTION96.11

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