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- PDB-7bn6: Crystal structure of G. sulphuraria ene-reductase GsOYE in comple... -

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Basic information

Entry
Database: PDB / ID: 7bn6
TitleCrystal structure of G. sulphuraria ene-reductase GsOYE in complex with b-angelica lactone
ComponentsNADPH2 dehydrogenase-like protein
KeywordsOXIDOREDUCTASE / NADPH dehydrogenase
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 / (2~{R})-2-methyl-2~{H}-furan-5-one / NADPH2 dehydrogenase-like protein
Similarity search - Component
Biological speciesGaldieria sulphuraria (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 21, 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)91,9995
Polymers90,9882
Non-polymers1,0113
Water4,540252
1
A: NADPH2 dehydrogenase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0493
Polymers45,4941
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)45,9512
Polymers45,4941
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.703, 76.482, 86.072
Angle α, β, γ (deg.)90.000, 93.038, 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: 45494.203 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 (E. coli) / References: UniProt: M2XAQ9
#2: Chemical ChemComp-U5N / (2~{R})-2-methyl-2~{H}-furan-5-one


Mass: 98.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O2
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.1 Å3/Da / Density % sol: 41.38 %
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 EIGER2 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: 1.5→48.48 Å / Num. obs: 288040 / % possible obs: 97.93 % / Redundancy: 2.5 % / Biso Wilson estimate: 17.43 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.049 / Net I/σ(I): 10.8
Reflection shellResolution: 1.5→1.554 Å / Rmerge(I) obs: 0.4332 / Mean I/σ(I) obs: 1.83 / Num. unique obs: 27828 / CC1/2: 0.702

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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: 1.5→48.48 Å / SU ML: 0.2117 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.4495
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.255 10247 5.18 %
Rwork0.2319 187710 -
obs0.2331 197957 85.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.8 Å2
Refinement stepCycle: LAST / Resolution: 1.5→48.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6083 0 69 252 6404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00776307
X-RAY DIFFRACTIONf_angle_d1.04078554
X-RAY DIFFRACTIONf_chiral_restr0.0691896
X-RAY DIFFRACTIONf_plane_restr0.00791128
X-RAY DIFFRACTIONf_dihedral_angle_d25.03552383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.34273340.31156149X-RAY DIFFRACTION84.45
1.52-1.530.33693520.30626218X-RAY DIFFRACTION84.14
1.53-1.550.33673260.29956114X-RAY DIFFRACTION84.12
1.55-1.570.31233090.29266201X-RAY DIFFRACTION84.59
1.57-1.590.32493720.29196087X-RAY DIFFRACTION83.83
1.59-1.620.33283350.29446157X-RAY DIFFRACTION84.24
1.62-1.640.32833110.29026081X-RAY DIFFRACTION83.46
1.64-1.660.33772950.28586124X-RAY DIFFRACTION82.34
1.66-1.690.29912900.28555949X-RAY DIFFRACTION81.31
1.69-1.720.29383530.28115939X-RAY DIFFRACTION81.25
1.72-1.750.32283450.27065958X-RAY DIFFRACTION83.17
1.75-1.780.25643030.26526140X-RAY DIFFRACTION82.18
1.78-1.810.28813280.25296082X-RAY DIFFRACTION83.58
1.81-1.850.28713840.24186337X-RAY DIFFRACTION87.21
1.85-1.890.25853870.24376401X-RAY DIFFRACTION87.84
1.89-1.930.26493540.23796275X-RAY DIFFRACTION86.77
1.93-1.980.25284150.23936394X-RAY DIFFRACTION87.79
1.98-2.040.293750.24066424X-RAY DIFFRACTION87.89
2.04-2.10.29883220.24466420X-RAY DIFFRACTION87.07
2.1-2.160.25933580.24336379X-RAY DIFFRACTION88
2.16-2.240.27543060.23426361X-RAY DIFFRACTION86.44
2.24-2.330.26093370.24046282X-RAY DIFFRACTION85.83
2.33-2.440.25473350.246321X-RAY DIFFRACTION86.46
2.44-2.560.26243320.23596231X-RAY DIFFRACTION85.24
2.56-2.730.25283550.22996273X-RAY DIFFRACTION85.52
2.73-2.940.25523520.23556326X-RAY DIFFRACTION86.76
2.94-3.230.27712860.23716418X-RAY DIFFRACTION87.17
3.23-3.70.22833390.21296412X-RAY DIFFRACTION87.53
3.7-4.660.19493950.18866643X-RAY DIFFRACTION91.19
4.66-48.480.21973620.18916614X-RAY DIFFRACTION90.39

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