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- PDB-4ide: Structure of the Fragaria x ananassa enone oxidoreductase in comp... -

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Basic information

Entry
Database: PDB / ID: 4ide
TitleStructure of the Fragaria x ananassa enone oxidoreductase in complex with NADP+ and EDHMF
ComponentsRipening-induced protein
KeywordsOXIDOREDUCTASE / medium chain dehydrogenase/reductase family / zinc-independent / Rossmann fold / Enone oxidoreductase / furaneol / hydride transfer / NADPH / NADH / EDHMF / (2E)-ethylidene-4-hydroxy-5-methyl-3(2H)-furanone
Function / homology
Function and homology information


2-methylene-furan-3-one reductase / furaneol oxidoreductase activity / zinc ion binding
Similarity search - Function
NADPH-dependent oxidoreductase AOR-like / Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / Zinc-binding dehydrogenase / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase ...NADPH-dependent oxidoreductase AOR-like / Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / Zinc-binding dehydrogenase / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-3XX / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2-methylene-furan-3-one reductase
Similarity search - Component
Biological speciesFragaria vesca (wild strawberry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSchiefner, A. / Skerra, A.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural basis for the enzymatic formation of the key strawberry flavor compound 4-hydroxy-2,5-dimethyl-3(2H)-furanone
Authors: Schiefner, A. / Sinz, Q. / Neumaier, I. / Schwab, W. / Skerra, A.
History
DepositionDec 12, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ripening-induced protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4816
Polymers35,3771
Non-polymers1,1045
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.962, 69.962, 174.511
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ripening-induced protein / FAEO


Mass: 35377.387 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 17-336
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fragaria vesca (wild strawberry) / Gene: gene28406 / Plasmid: pASK-IBA5plus / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: O23939

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Non-polymers , 5 types, 381 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-3XX / (2E)-2-ethylidene-4-hydroxy-5-methylfuran-3(2H)-one


Mass: 140.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsNATURAL VARIANT AT THIS POSITION

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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: 3.02 Å3/Da / Density % sol: 59.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 21-16% (w/v) PEG3350, 0.2M Li2SO4, 0.1M Tris/HCl pH 7.0-8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 28, 2011
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 58034 / Num. obs: 58034 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8.05 % / Biso Wilson estimate: 26.003 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 23.43
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.6-1.70.5710.8053.3777132948394800.859100
1.7-1.80.350.4855.4861236751575140.518100
1.8-20.1780.24310.298858810932109060.25999.8
2-30.0510.07128.5816902520920208830.07699.8
3-40.0180.03157.6741173522252220.033100
4-60.0120.02468.921370277127700.025100
6-80.0120.02267.9752247067060.024100
8-100.0120.02269.1218302692680.02499.6
10-300.0120.02167.5218253022850.02494.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345data collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IDC

4idc


Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.1673 / WRfactor Rwork: 0.1401 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9078 / SU B: 2.247 / SU ML: 0.042 / SU R Cruickshank DPI: 0.0622 / SU Rfree: 0.0658 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1797 1763 3 %RANDOM
Rwork0.1513 ---
all0.1522 58034 --
obs0.1522 58034 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.14 Å2 / Biso mean: 23.3283 Å2 / Biso min: 7.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2--0.27 Å2-0 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2405 0 71 376 2852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022558
X-RAY DIFFRACTIONr_bond_other_d0.0010.022494
X-RAY DIFFRACTIONr_angle_refined_deg2.0712.0243496
X-RAY DIFFRACTIONr_angle_other_deg0.8983.0015787
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7455329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.77525.11984
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.91315416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.322156
X-RAY DIFFRACTIONr_chiral_restr0.1250.2414
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212805
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02493
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 113 -
Rwork0.211 4093 -
all-4206 -
obs--99.98 %
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)
12.1107-0.90250.92412.6639-0.3772.4306-0.0372-0.37820.0570.28770.0382-0.0461-0.12170.1428-0.0010.0458-0.0159-0.01970.1422-0.02450.0548-25.721222.149118.6267
21.499-0.74640.42142.0118-0.60642.07670.079-0.157-0.0764-0.17140.00870.13940.0791-0.0163-0.08780.016-0.0085-0.01490.06170.01870.0166-32.432116.89559.6094
32.4361-0.02760.92781.63130.36733.18770.03810.2532-0.12-0.21070.0725-0.20580.17390.5229-0.11060.12460.0358-0.01090.1152-0.03930.0515-29.368213.3427-16.7137
41.0641-0.25360.88211.7406-0.02474.42820.03910.1517-0.0036-0.23840.0754-0.1245-0.15430.2306-0.11450.0738-0.0033-0.00770.0498-0.020.0366-36.362520.1211-14.2842
511.12856.1286-4.978620.57132.336313.2728-0.26340.371-0.6571-0.87010.28240.30280.5369-0.0136-0.0190.21710.0458-0.10220.0569-0.01650.1487-32.00650.8923-5.3589
61.54040.09480.43842.6531-0.29551.88250.05970.14470.0878-0.2509-0.0347-0.20160.06050.4133-0.0250.03490.02350.03080.16630.02930.0637-17.670315.99022.5902
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 41
2X-RAY DIFFRACTION2A42 - 149
3X-RAY DIFFRACTION3A150 - 222
4X-RAY DIFFRACTION4A223 - 279
5X-RAY DIFFRACTION5A280 - 286
6X-RAY DIFFRACTION6A287 - 321

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