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- PDB-8ov8: Crystal structure of Ene-reductase 1 from black poplar mushroom i... -

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Basic information

Entry
Database: PDB / ID: 8ov8
TitleCrystal structure of Ene-reductase 1 from black poplar mushroom in complex to NADP
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Ene-reductase 1
Similarity search - Component
Biological speciesCyclocybe aegerita (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKorf, L. / Essen, L.-O. / Karrer, D. / Ruehl, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB987 Germany
Citation
Journal: 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.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionApr 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 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
B: Ene-reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,35310
Polymers76,3622
Non-polymers1,9908
Water10,827601
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-85 kcal/mol
Surface area29980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.420, 99.729, 103.099
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3 through 22 or resid 24...
d_2ens_1(chain "B" and (resid 3 through 22 or resid 24...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PROGLYA2 - 21
d_12ens_1THRPROA23 - 63
d_13ens_1LYSSERA66 - 67
d_14ens_1SERLEUA69 - 118
d_15ens_1ALAILEA120 - 121
d_16ens_1ASNPROA123 - 153
d_17ens_1GLNGLUA155 - 190
d_18ens_1LYSLYSA192 - 197
d_19ens_1VALGLYA199 - 231
d_110ens_1THRLEUA233 - 238
d_111ens_1ALAVALA240 - 281
d_112ens_1ARGTYRA283 - 288
d_113ens_1ALATYRA290 - 307
d_114ens_1GLULEUA309 - 342
d_21ens_1PROGLYB1 - 20
d_22ens_1THRPROB22 - 62
d_23ens_1LYSSERB65 - 66
d_24ens_1SERLEUB68 - 117
d_25ens_1ALAILEB119 - 120
d_26ens_1ASNPROB122 - 152
d_27ens_1GLNGLUB154 - 189
d_28ens_1LYSLYSB191 - 196
d_29ens_1VALGLYB198 - 230
d_210ens_1THRLEUB232 - 237
d_211ens_1ALAVALB239 - 280
d_212ens_1ARGTYRB282 - 287
d_213ens_1ALATYRB289 - 306
d_214ens_1GLULEUB308 - 341

NCS oper: (Code: givenMatrix: (-0.991721349102, 0.103153634119, 0.0764728285245), (0.0765076384803, -0.00362492261965, 0.997062405865), (0.103127818695, 0.994658829802, -0.00429712779636)Vector: 15. ...NCS oper: (Code: given
Matrix: (-0.991721349102, 0.103153634119, 0.0764728285245), (0.0765076384803, -0.00362492261965, 0.997062405865), (0.103127818695, 0.994658829802, -0.00429712779636)
Vector: 15.9281064014, 21.3377231613, -22.596708346)

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Components

#1: Protein Ene-reductase 1


Mass: 38181.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyclocybe aegerita (fungus) / Gene: ENR1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8A1QR26
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 601 / 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: 2.81 Å3/Da / Density % sol: 56.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M Bicine pH 9.0, 1.6 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999869 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999869 Å / Relative weight: 1
ReflectionResolution: 1.9→45.79 Å / Num. obs: 67607 / % possible obs: 99 % / Redundancy: 6.5 % / Biso Wilson estimate: 36.62 Å2 / CC1/2: 0.996 / Net I/σ(I): 8.1
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 67237 / CC1/2: 0.733 / CC star: 0.92

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Processing

Software
NameVersionClassification
PHENIXdev_4788refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→45.79 Å / SU ML: 0.2248 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.3247
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2071 3438 5.11 %
Rwork0.1691 63795 -
obs0.171 67233 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.21 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5365 0 122 601 6088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00745718
X-RAY DIFFRACTIONf_angle_d0.90477798
X-RAY DIFFRACTIONf_chiral_restr0.0528843
X-RAY DIFFRACTIONf_plane_restr0.00671001
X-RAY DIFFRACTIONf_dihedral_angle_d17.75762051
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.630318266481 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.40541240.41872309X-RAY DIFFRACTION90.14
1.93-1.950.39781300.34882465X-RAY DIFFRACTION95.26
1.95-1.980.31981130.322535X-RAY DIFFRACTION97.46
1.98-2.010.3531320.29552474X-RAY DIFFRACTION98.45
2.01-2.050.33021370.27962562X-RAY DIFFRACTION99.16
2.05-2.080.34011500.27342545X-RAY DIFFRACTION99.19
2.08-2.120.27621350.24172546X-RAY DIFFRACTION99.44
2.12-2.160.2771220.23542573X-RAY DIFFRACTION99.41
2.16-2.20.25541370.23382577X-RAY DIFFRACTION99.38
2.2-2.250.30381600.25782420X-RAY DIFFRACTION95.77
2.25-2.310.23361540.2012499X-RAY DIFFRACTION97.93
2.31-2.360.27931400.19122570X-RAY DIFFRACTION99.63
2.36-2.430.24051270.18712501X-RAY DIFFRACTION97.3
2.43-2.50.23421320.18242582X-RAY DIFFRACTION99.6
2.5-2.580.20811240.17162580X-RAY DIFFRACTION99.56
2.58-2.670.24861410.17832571X-RAY DIFFRACTION99.56
2.67-2.780.22541390.19312602X-RAY DIFFRACTION99.46
2.78-2.90.25131340.18332583X-RAY DIFFRACTION99.6
2.9-3.060.21171270.18222580X-RAY DIFFRACTION99.45
3.06-3.250.21541360.17842616X-RAY DIFFRACTION99.53
3.25-3.50.23331590.16462513X-RAY DIFFRACTION96.85
3.5-3.850.16411450.14372588X-RAY DIFFRACTION99.02
3.85-4.410.16151600.12072612X-RAY DIFFRACTION99.32
4.41-5.550.13541430.11422664X-RAY DIFFRACTION99.33
5.55-45.790.17061370.14292728X-RAY DIFFRACTION97.38
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)
11.09885364334-0.5000449004620.3213241120881.002410060250.524182374380.8103780885960.03265450858930.2646455022960.0204347868457-0.2545681497550.08079179604370.202692885601-0.0644246557111-0.3889222787140.0003511726897330.512329050154-0.02298287303680.03924218429720.62148797730.127270741890.446778182765.2065938810854.478642552-14.8183303376
20.795076081308-0.262371979812-0.06880125610071.40208433856-0.4568983930821.517781009150.008126532982840.06823594148120.107794041864-0.088694006460.0400009647082-0.18111428927-0.0398153189210.0590060851367-3.15582092738E-50.362723650516-0.03394500596130.07105447070970.3741302590840.002632706928310.4046694580119.565654282347.69582941892.35540040938
30.2886193409240.01923775163010.2842637444790.0878691272455-0.07782529977670.324744968702-0.1630299522260.07149887770520.3180027458310.1699426789220.2009276365380.188708304448-0.5488747084270.2340696684710.0006411899881210.749806435376-0.1389505816580.1440280350970.5946053647540.05911525722170.62057251936722.352808105962.4848569501-15.974182188
41.63359299625-0.3670200609860.1148475591281.619813335730.2612572544470.6809180600320.21345790762-0.267644427296-0.4851145877370.25065921646-0.177375670965-0.6305373475490.1922749166430.448972030929-0.0004583535836150.537789123976-0.143825058641-0.1589644231620.5657525905130.1945968063450.70329963509315.29855827487.9013302037435.4072956966
51.460168315930.4880844259560.5372807029731.8729825354-0.2962940862811.423763977260.129044355799-0.271482579014-0.0247266342754-0.0132372890611-0.1164170662120.04494118192770.00676594760028-0.183841431791-0.0004329185266540.302275372025-0.06645338904750.01161261557070.400216090097-0.0003081456476660.3324671550.079760684527426.520941168924.9145617285
60.358803374157-0.194093552018-0.0985607803130.736850790838-0.3986988238710.33483659666-0.154244150816-0.337870745429-0.02087095915130.776332287646-0.1849285395110.117947631818-0.014670513343-0.0716664129892-0.002903056782410.746189675185-0.1631783467770.003823738422780.5997277014760.08134708318210.548688375968-1.65660613237.2157139752739.9721252439
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 90 )AA2 - 901 - 89
22chain 'A' and (resid 91 through 327 )AA91 - 32790 - 326
33chain 'A' and (resid 328 through 350 )AA328 - 350327 - 349
44chain 'B' and (resid 3 through 113 )BB3 - 1131 - 111
55chain 'B' and (resid 114 through 327 )BB114 - 327112 - 325
66chain 'B' and (resid 328 through 350 )BB328 - 350326 - 348

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