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- PDB-4ida: Structure of the Fragaria x ananassa enone oxidoreductase in its ... -

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Basic information

Entry
Database: PDB / ID: 4ida
TitleStructure of the Fragaria x ananassa enone oxidoreductase in its apo form
ComponentsRipening-induced protein
KeywordsOXIDOREDUCTASE / medium chain dehydrogenase/reductase family / zinc-independent / Rossmann fold / Enone oxidoreductase / furaneol / hydride transfer / NADPH / NADH
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
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 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

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Assembly

Deposited unit
A: Ripening-induced protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7566
Polymers35,3771
Non-polymers3785
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.376, 70.376, 172.882
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#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
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O
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: 3.03 Å3/Da / Density % sol: 59.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 28-25 % (w/v) PEG3350, 0.2M Li2SO4, 0.1M Citrate/NaOH pH 5.5-6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 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: 58211 / Num. obs: 58211 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 9.64 % / Biso Wilson estimate: 29.679 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 27.24
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
1.6-1.70.5920.8132.9792619947894740.858100
1.7-1.80.3260.455.2773767754275420.475100
1.8-1.90.1960.2728.5659340605460540.287100
1.9-20.1190.1713.6447928489148910.18100
2-30.040.05934.1720344120976209750.062100
3-40.0130.02769.0848563523352320.029100
4-60.0090.01979.8925208278427840.02100
6-80.0080.01679.3262057087080.017100
8-100.0070.01479.221822672660.01599.6
10-300.0070.01374.6320643042850.01493.8

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Processing

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

4idc


Resolution: 1.6→29.59 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.1679 / WRfactor Rwork: 0.1497 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9132 / SU B: 2.276 / SU ML: 0.041 / SU R Cruickshank DPI: 0.0621 / SU Rfree: 0.0623 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1732 1771 3 %RANDOM
Rwork0.1545 ---
all0.1551 58211 --
obs0.1551 58211 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.63 Å2 / Biso mean: 26.726 Å2 / Biso min: 12.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20 Å2
2--0.53 Å2-0 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2405 0 22 306 2733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192534
X-RAY DIFFRACTIONr_bond_other_d0.0010.022498
X-RAY DIFFRACTIONr_angle_refined_deg1.9912.0013456
X-RAY DIFFRACTIONr_angle_other_deg0.92335801
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6545336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24725.05787
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.53415426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.545157
X-RAY DIFFRACTIONr_chiral_restr0.1250.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212821
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02486
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 119 -
Rwork0.235 4087 -
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)
122.46681.4061-5.09983.601-3.96584.94320.1141-1.08750.4709-0.08070.44660.47950.0721-0.2857-0.56070.32480.06520.02210.58450.07990.448-33.60977.497428.913
21.3932-0.39340.5342.4566-0.4851.5686-0.012-0.18550.0498-0.0081-0.00180.0391-0.04510.04820.01380.0054-0.0046-0.01540.12340.02070.0613-29.998820.519412.3114
31.03710.09121.75120.04540.04234.55990.0938-0.0601-0.1923-0.0703-0.010.00710.3939-0.0208-0.08380.17140.0112-0.06430.04630.00990.1283-34.175211.6457-5.0138
42.93230.380.52643.2803-0.15593.1187-0.03810.3218-0.0651-0.290.0797-0.53190.19980.6241-0.04160.14990.02630.00040.2282-0.05090.1588-26.56814.283-18.6594
50.945-0.24510.77751.3281-0.49413.6860.01080.1385-0.0515-0.25650.0476-0.10580.07640.1786-0.05830.0949-0.0146-0.03530.0944-0.01270.0928-35.712818.6692-13.547
62.6587-0.6059-0.13654.98061.08342.69850.06380.24770.115-0.4431-0.0357-0.2881-0.0390.4642-0.02820.04250.02870.03480.2410.04680.1286-16.206517.00112.8611
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 8
2X-RAY DIFFRACTION2A9 - 133
3X-RAY DIFFRACTION3A134 - 164
4X-RAY DIFFRACTION4A165 - 222
5X-RAY DIFFRACTION5A223 - 287
6X-RAY DIFFRACTION6A288 - 321

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