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- PDB-7bo0: Crystal structure of ene-reductase GsOYE from Galdieria sulphurar... -

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Basic information

Entry
Database: PDB / ID: 7bo0
TitleCrystal structure of ene-reductase GsOYE from Galdieria sulphuraria in complex with alpha-angelica lactone
ComponentsNADPH2 dehydrogenase-like protein
KeywordsOXIDOREDUCTASE / NADPH dehydrogenase / ene-reductase
Function / homology
Function and homology information


FMN binding / oxidoreductase activity / metal ion binding / cytosol
Similarity search - Function
Oxidoreductase Oye-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase-type TIM barrel
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / 5-methyl-3~{H}-furan-2-one / NADPH2 dehydrogenase-like protein
Similarity search - Component
Biological speciesGaldieria sulphuraria (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 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 23, 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: NADPH2 dehydrogenase-like protein
B: NADPH2 dehydrogenase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2745
Polymers90,2642
Non-polymers1,0113
Water8,071448
1
A: NADPH2 dehydrogenase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6863
Polymers45,1321
Non-polymers5542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NADPH2 dehydrogenase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5882
Polymers45,1321
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.820, 76.690, 86.930
Angle α, β, γ (deg.)90.000, 92.969, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein NADPH2 dehydrogenase-like protein


Mass: 45131.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Galdieria sulphuraria (eukaryote) / Gene: Gasu_54250 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M2XAQ9
#2: Chemical ChemComp-U6W / 5-methyl-3~{H}-furan-2-one / alpha-angelica lactone


Mass: 98.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C5H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C17H21N4O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.18 Å3/Da / Density % sol: 43.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M MgCl2 hexahydrate or 0.2 M CaCl2 dihydrate, 0.1 M MES pH 6.0, 20 % w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.63→56.74 Å / Num. obs: 154172 / % possible obs: 89.13 % / Redundancy: 1.9 % / Biso Wilson estimate: 18.65 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.042 / Net I/σ(I): 12.22
Reflection shellResolution: 1.63→1.689 Å / Rmerge(I) obs: 0.3119 / Num. unique obs: 17504 / CC1/2: 0.813

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S0G

6s0g


Resolution: 1.63→56.74 Å / SU ML: 0.2388 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.0458
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2619 4080 4.93 %
Rwork0.2367 78621 -
obs0.238 82701 89.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.4 Å2
Refinement stepCycle: LAST / Resolution: 1.63→56.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6102 0 69 448 6619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00836317
X-RAY DIFFRACTIONf_angle_d1.17578565
X-RAY DIFFRACTIONf_chiral_restr0.2517896
X-RAY DIFFRACTIONf_plane_restr0.00731129
X-RAY DIFFRACTIONf_dihedral_angle_d26.37832386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.650.3491670.31092956X-RAY DIFFRACTION99.4
1.65-1.670.341580.31563070X-RAY DIFFRACTION99.78
1.67-1.690.36311490.30442962X-RAY DIFFRACTION99.81
1.69-1.710.33421620.31713062X-RAY DIFFRACTION99.91
1.71-1.740.40621770.34792909X-RAY DIFFRACTION96.86
1.74-1.760.31311530.27643013X-RAY DIFFRACTION99.81
1.76-1.790.29591500.2743025X-RAY DIFFRACTION99.75
1.79-1.820.28931590.25813011X-RAY DIFFRACTION99.81
1.82-1.850.29231790.25433021X-RAY DIFFRACTION99.75
1.85-1.880.26181790.27372990X-RAY DIFFRACTION98.75
1.88-1.90.47971090.35481928X-RAY DIFFRACTION89.42
1.93-1.940.3331680.28851276X-RAY DIFFRACTION89.6
1.95-1.990.30731280.27342524X-RAY DIFFRACTION96.86
1.99-2.030.29621540.2513023X-RAY DIFFRACTION99.22
2.03-2.080.2988580.25881388X-RAY DIFFRACTION45.37
2.08-2.130.25721380.25963010X-RAY DIFFRACTION99.12
2.13-2.190.28191560.24113033X-RAY DIFFRACTION99.28
2.19-2.230.30491000.24771906X-RAY DIFFRACTION95.12
2.27-2.330.30811170.28162311X-RAY DIFFRACTION93.53
2.33-2.410.24081550.23863034X-RAY DIFFRACTION99.69
2.41-2.510.27811690.25362959X-RAY DIFFRACTION98.4
2.51-2.620.30121340.25792989X-RAY DIFFRACTION97.2
2.62-2.760.23291080.24252147X-RAY DIFFRACTION70.18
2.76-2.930.30971350.23652988X-RAY DIFFRACTION97.87
2.93-3.160.26121530.23613016X-RAY DIFFRACTION98.42
3.16-3.470.25631300.22652592X-RAY DIFFRACTION84.67
3.47-3.980.19891220.20232434X-RAY DIFFRACTION78.99
3.98-5.010.19241760.17832987X-RAY DIFFRACTION97.9
5.01-56.740.19251370.18083057X-RAY DIFFRACTION96.5

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