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- PDB-6s31: Crystal structure of ene-reductase GsOYE from Galdieria sulphurar... -

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Basic information

Entry
Database: PDB / ID: 6s31
TitleCrystal structure of ene-reductase GsOYE from Galdieria sulphuraria in complex with 4-Hydroxybenzaldehyde
ComponentsNADPH2 dehydrogenase-like protein
KeywordsFLAVOPROTEIN / ene-reductase / Old Yellow Enzyme / Biocatalysis
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / FMN binding / 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 / P-HYDROXYBENZALDEHYDE / NADPH2 dehydrogenase-like protein
Similarity search - Component
Biological speciesGaldieria sulphuraria (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 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 23, 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 2.0Feb 3, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Source and taxonomy
Category: atom_site / entity_src_gen ...atom_site / entity_src_gen / pdbx_nonpoly_scheme / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_nonpoly_scheme.auth_seq_num / _struct_ref_seq_dif.details
Revision 2.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Mar 4, 2026Group: Refinement description / Structure summary
Category: pdbx_entry_details / pdbx_initial_refinement_model
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADPH2 dehydrogenase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2045
Polymers45,3811
Non-polymers8234
Water8,053447
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint8 kcal/mol
Surface area14520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.048, 76.293, 88.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-875-

HOH

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Components

#1: Protein NADPH2 dehydrogenase-like protein


Mass: 45381.043 Da / Num. of mol.: 1
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-HBA / P-HYDROXYBENZALDEHYDE


Mass: 122.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H6O2
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.23 Å3/Da / Density % sol: 44.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 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: ID23-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.63→57.7 Å / Num. obs: 48778 / % possible obs: 99.72 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.21 / Net I/σ(I): 9
Reflection shellResolution: 1.63→1.69 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 4758 / % possible all: 99.12

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2SOG

2sog


Resolution: 1.63→57.679 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.85
RfactorNum. reflection% reflection
Rfree0.2034 4699 5.08 %
Rwork0.1728 --
obs0.1743 48778 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.63→57.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3032 0 58 447 3537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073237
X-RAY DIFFRACTIONf_angle_d0.9494386
X-RAY DIFFRACTIONf_dihedral_angle_d12.2722660
X-RAY DIFFRACTIONf_chiral_restr0.057450
X-RAY DIFFRACTIONf_plane_restr0.006578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.629-1.64740.22741550.21282748X-RAY DIFFRACTION96
1.6474-1.66670.25841590.20312969X-RAY DIFFRACTION99
1.6667-1.68710.21431630.20412871X-RAY DIFFRACTION99
1.6871-1.70840.25881650.21332873X-RAY DIFFRACTION99

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