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- PDB-6s0g: Crystal structure of ene-reductase GsOYE from Galdieria sulphuraria -

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Basic information

Entry
Database: PDB / ID: 6s0g
TitleCrystal structure of ene-reductase GsOYE from Galdieria sulphuraria
ComponentsNADPH2 dehydrogenase-like protein
KeywordsFLAVOPROTEIN / ene-reductase / Old Yellow Enzyme / Biocatalysis
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 class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / NADPH2 dehydrogenase-like protein
Similarity search - Component
Biological speciesGaldieria sulphuraria (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsRobescu, M.R. / Niero, M. / Hall, M. / Bergantino, E. / Cendron, L.
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2020
Title: Two new ene-reductases from photosynthetic extremophiles enlarge the panel of old yellow enzymes: CtOYE and GsOYE.
Authors: Robescu, M.S. / Niero, M. / Hall, M. / Cendron, L. / Bergantino, E.
History
DepositionJun 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: NADPH2 dehydrogenase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0484
Polymers45,4941
Non-polymers5543
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-11 kcal/mol
Surface area14700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.745, 76.662, 88.596
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein NADPH2 dehydrogenase-like protein


Mass: 45494.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Galdieria sulphuraria (eukaryote) / Gene: Gasu_54250 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M2XAQ9
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.12 Å3/Da / Density % sol: 41.92 %
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: ID23-2 / Wavelength: 1.0725 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0725 Å / Relative weight: 1
ReflectionResolution: 1.45→45.61 Å / Num. obs: 880814 / % possible obs: 99.8 % / Redundancy: 12.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.03 / Net I/σ(I): 18
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 45283 / CC1/2: 0.993 / Rpim(I) all: 0.26 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GWJ

1gwj


Resolution: 1.45→45.61 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 18.49
RfactorNum. reflection% reflection
Rfree0.1958 3445 4.98 %
Rwork0.1868 --
obs0.1872 69132 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→45.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3051 0 36 228 3315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0343206
X-RAY DIFFRACTIONf_angle_d1.0414345
X-RAY DIFFRACTIONf_dihedral_angle_d14.1561962
X-RAY DIFFRACTIONf_chiral_restr0.084453
X-RAY DIFFRACTIONf_plane_restr0.013574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.46990.2481350.23522591X-RAY DIFFRACTION100
1.4699-1.49090.23981410.22822589X-RAY DIFFRACTION100
1.4909-1.51310.2761370.21422610X-RAY DIFFRACTION100
1.5131-1.53680.23091650.20932568X-RAY DIFFRACTION100
1.5368-1.5620.23781340.21162568X-RAY DIFFRACTION100
1.562-1.58890.23471310.21092618X-RAY DIFFRACTION100
1.5889-1.61780.23471270.20072617X-RAY DIFFRACTION100
1.6178-1.64890.21241330.20612585X-RAY DIFFRACTION100
1.6489-1.68260.22291210.19742592X-RAY DIFFRACTION100
1.6826-1.71920.20021430.19422620X-RAY DIFFRACTION100
1.7192-1.75920.21031380.19552579X-RAY DIFFRACTION100
1.7592-1.80320.20071460.19592608X-RAY DIFFRACTION100
1.8032-1.85190.2111240.19562619X-RAY DIFFRACTION100
1.8519-1.90640.18831380.19012618X-RAY DIFFRACTION100
1.9064-1.9680.20491210.19162647X-RAY DIFFRACTION100
1.968-2.03830.19281260.19022618X-RAY DIFFRACTION100
2.0383-2.11990.24491410.19022628X-RAY DIFFRACTION100
2.1199-2.21640.19891380.19092627X-RAY DIFFRACTION100
2.2164-2.33320.1971430.1892620X-RAY DIFFRACTION100
2.3332-2.47940.19731400.19492644X-RAY DIFFRACTION100
2.4794-2.67080.1961480.18762627X-RAY DIFFRACTION100
2.6708-2.93960.17951460.18882657X-RAY DIFFRACTION100
2.9396-3.36490.19711400.18962683X-RAY DIFFRACTION100
3.3649-4.2390.16811460.16822703X-RAY DIFFRACTION100
4.239-47.81010.16931430.16112851X-RAY DIFFRACTION100

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