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- PDB-6s23: Crystal structure of ene-reductase GsOYE from Galleria sulphurari... -

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Basic information

Entry
Database: PDB / ID: 6s23
TitleCrystal structure of ene-reductase GsOYE from Galleria sulphuraria in complex with 2-methyl-cyclopenten-1-one
ComponentsNADPH2 dehydrogenase-like protein
KeywordsOXIDOREDUCTASE / ene-reductase / Old Yellow enzyme
Function / homology
Function and homology information


FMN binding / oxidoreductase activity
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 / 2-methylcyclopenta-2,4-dien-1-one / NADPH2 dehydrogenase-like protein
Similarity search - Component
Biological speciesGaldieria sulphuraria (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsRobescu, M.S. / 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 20, 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 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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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)92,2088
Polymers90,9882
Non-polymers1,2196
Water1,72996
1
A: NADPH2 dehydrogenase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1394
Polymers45,4941
Non-polymers6453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NADPH2 dehydrogenase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0694
Polymers45,4941
Non-polymers5753
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.693, 76.421, 86.334
Angle α, β, γ (deg.)90.00, 93.40, 90.00
Int Tables number4
Space group name H-MP1211

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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-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-KSW / 2-methylcyclopenta-2,4-dien-1-one


Mass: 94.111 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H6O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.05 Å3/Da / Density % sol: 40.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M MgCl2 hexahydrate, 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: 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: 2.38→57.18 Å / Num. obs: 29511 / % possible obs: 99.4 % / Redundancy: 3.2 % / Net I/σ(I): 14.2
Reflection shellResolution: 2.38→2.47 Å / Num. unique obs: 3122 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S0G

6s0g


Resolution: 2.38→50.01 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.821 / SU B: 19.572 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.734 / ESU R Free: 0.293
RfactorNum. reflection% reflectionSelection details
Rfree0.25554 1435 4.9 %RANDOM
Rwork0.20981 ---
obs0.21203 28059 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.001 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å20.29 Å2
2---1.07 Å20 Å2
3---1.84 Å2
Refinement stepCycle: LAST / Resolution: 2.38→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6083 0 84 96 6263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0126313
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.841.6628558
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.295758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91720.876388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.719151047
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8891563
X-RAY DIFFRACTIONr_chiral_restr0.1320.2778
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024996
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it00.053038
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it00.0753794
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it00.053275
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined0.1560.6739769
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.38→2.442 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 116 -
Rwork0.201 2048 -
obs--99.72 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5378-0.1105-0.46881.60040.11721.12010.02750.2030.0484-0.1818-0.04110.0518-0.0033-0.1510.01360.13-0.00160.01930.0405-0.00350.0094-13.787-11.16643.379
22.6602-0.2610.15591.3752-0.08371.1707-0.0258-0.1264-0.13670.09040.05290.09380.0014-0.1077-0.0270.11520.01980.01180.01890.01070.0124-16.25213.06485.653
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 1004
2X-RAY DIFFRACTION2B1 - 1004

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