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- PDB-8ov9: Crystal structure of Ene-reductase 1 from black poplar mushroom -

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Basic information

Entry
Database: PDB / ID: 8ov9
TitleCrystal structure of Ene-reductase 1 from black poplar mushroom
ComponentsEne-reductase 1
KeywordsOXIDOREDUCTASE / NAD/NADP-dependent dehydrogenase / ene/yne-reductase / fungal secondary metabolites
Function / homology
Function and homology information


2-alkenal reductase [NAD(P)+] / oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
Similarity search - Function
Oxidoreductase, N-terminal domain / Medium-chain dehydrogenase/reductase / N-terminal domain of oxidoreductase / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Biological speciesCyclocybe aegerita (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsKorf, L. / Essen, L.-O. / Karrer, D. / Ruehl, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB987 Germany
CitationJournal: To Be Published
Title: Shifting the substrate scope of an ene/yne-reductase by loop engineering
Authors: Karrer, D. / Wedler, E. / Mewe, C. / Gand, M. / Vogt, M.S. / Korf, L. / Essen, L.-O. / Ruehl, M.
History
DepositionApr 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ene-reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6426
Polymers38,1811
Non-polymers4605
Water11,440635
1
A: Ene-reductase 1
hetero molecules

A: Ene-reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,28312
Polymers76,3622
Non-polymers92110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area4560 Å2
ΔGint-29 kcal/mol
Surface area29500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.310, 59.308, 208.365
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-1122-

HOH

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Components

#1: Protein Ene-reductase 1


Mass: 38181.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyclocybe aegerita (fungus) / Gene: ENR1 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: A0A8A1QR26
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 635 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.36 Å3/Da / Density % sol: 47.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M Bicine pH 9.0, 1.6 M Ammonium sulfate 9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 12, 2020
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.41→41.58 Å / Num. obs: 867680 / % possible obs: 97.3 % / Redundancy: 12.8 % / Biso Wilson estimate: 13.39 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06758 / Rpim(I) all: 0.01922 / Rrim(I) all: 0.07033 / Net I/σ(I): 21.57
Reflection shellResolution: 1.41→1.43 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.4442 / Mean I/σ(I) obs: 2.99 / Num. unique obs: 6759 / CC1/2: 0.856 / CC star: 0.96 / Rpim(I) all: 0.2288 / Rrim(I) all: 0.5014 / % possible all: 50.76

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Processing

Software
NameVersionClassification
PHENIXdev_4788refinement
PHENIXdev_4788refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.41→41.58 Å / SU ML: 0.0969 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.308
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1527 3360 4.96 %
Rwork0.1245 64403 -
obs0.1259 67763 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.04 Å2
Refinement stepCycle: LAST / Resolution: 1.41→41.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2615 0 30 635 3280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00852799
X-RAY DIFFRACTIONf_angle_d1.05083801
X-RAY DIFFRACTIONf_chiral_restr0.0802412
X-RAY DIFFRACTIONf_plane_restr0.0095494
X-RAY DIFFRACTIONf_dihedral_angle_d14.20521035
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.430.1868670.17121403X-RAY DIFFRACTION50.76
1.43-1.450.18861320.14312382X-RAY DIFFRACTION88.87
1.45-1.480.18821350.12472711X-RAY DIFFRACTION99.23
1.48-1.50.1761300.1192715X-RAY DIFFRACTION99.48
1.5-1.530.14581250.11472740X-RAY DIFFRACTION99.17
1.53-1.550.1461420.1132708X-RAY DIFFRACTION99.51
1.55-1.580.13081180.10842744X-RAY DIFFRACTION99.86
1.58-1.620.161380.1072747X-RAY DIFFRACTION99.97
1.62-1.650.1311560.10522734X-RAY DIFFRACTION100
1.65-1.690.1581300.10772730X-RAY DIFFRACTION100
1.69-1.730.16761620.10872753X-RAY DIFFRACTION99.62
1.73-1.780.14291300.10852685X-RAY DIFFRACTION99.51
1.78-1.830.13751380.11432734X-RAY DIFFRACTION99.65
1.83-1.890.16081580.11612776X-RAY DIFFRACTION100
1.89-1.960.1391520.11662715X-RAY DIFFRACTION100
1.96-2.040.13281680.112705X-RAY DIFFRACTION100
2.04-2.130.13031050.10952801X-RAY DIFFRACTION99.83
2.13-2.240.12931420.11292761X-RAY DIFFRACTION99.79
2.24-2.380.14571220.11082774X-RAY DIFFRACTION99.83
2.38-2.570.14281560.11982784X-RAY DIFFRACTION99.97
2.57-2.830.14471510.12812770X-RAY DIFFRACTION100
2.83-3.230.14081580.12682797X-RAY DIFFRACTION100
3.23-4.070.15931650.12822809X-RAY DIFFRACTION100
4.07-41.580.18151800.1622925X-RAY DIFFRACTION99.78

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