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

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Basic information

Entry
Database: PDB / ID: 4idc
TitleStructure of the Fragaria x ananassa enone oxidoreductase in complex with NADPH and HDMF
ComponentsRipening-induced protein
KeywordsOXIDOREDUCTASE / medium chain dehydrogenase/reductase family / zinc-independent / Rossmann fold / Enone oxidoreductase / furaneol / hydride transfer / NADPH / NADH / HDMF / 4-hydroxy-2 / 5-dimethyl-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
(2R)-4-hydroxy-2,5-dimethylfuran-3(2H)-one / Chem-NDP / 2-methylene-furan-3-one reductase
Similarity search - Component
Biological speciesFragaria vesca (wild strawberry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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

Downloads & links

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Assembly

Deposited unit
A: Ripening-induced protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4716
Polymers35,3771
Non-polymers1,0945
Water9,008500
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.241, 70.241, 174.984
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, 505 molecules

#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-1XX / (2R)-4-hydroxy-2,5-dimethylfuran-3(2H)-one


Mass: 128.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O3
#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.: 500 / 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: 3.05 Å3/Da / Density % sol: 59.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 21-16% (w/v) PEG 3350, 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: 14.1 / 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: 1.4→30 Å / Num. all: 86971 / Num. obs: 86971 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.89 % / Biso Wilson estimate: 20.382 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.97
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
1.4-1.50.4150.4963.7512727115973159710.531100
1.5-1.60.2280.2936.49983012307123060.313100
1.6-1.80.1260.17410.8713955117180171800.186100
1.8-20.0660.118.888805811016110160.107100
2-30.0330.05630.5716262521150211490.06100
3-40.0190.03840.1339144527752760.041100
4-60.0140.0342.4620734280128010.032100
6-80.0120.02241.6751907167160.023100
8-100.0090.01941.0818082672660.0299.6
10-300.010.01739.517833082900.01894.2

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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: 1IYZ

1iyz


Resolution: 1.4→29.58 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / WRfactor Rfree: 0.1567 / WRfactor Rwork: 0.1359 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9309 / SU B: 1.145 / SU ML: 0.025 / SU R Cruickshank DPI: 0.0404 / SU Rfree: 0.0429 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1596 2628 3 %RANDOM
Rwork0.1391 ---
all0.1398 86971 --
obs0.1398 86971 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.77 Å2 / Biso mean: 17.0414 Å2 / Biso min: 6.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å2-0 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.4→29.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2405 0 70 500 2975
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192600
X-RAY DIFFRACTIONr_bond_other_d0.0010.022533
X-RAY DIFFRACTIONr_angle_refined_deg2.0152.0233562
X-RAY DIFFRACTIONr_angle_other_deg0.8733.0015885
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7165339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.57525.11686
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.83715424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.037156
X-RAY DIFFRACTIONr_chiral_restr0.1250.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212871
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02503
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 176 -
Rwork0.22 6118 -
all-6294 -
obs--100 %
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)
119.173312.35937.601217.28375.9388.77650.6949-1.3994-0.10010.7416-0.66490.54410.8527-0.5473-0.030.31130.03150.03740.36750.09320.2662-35.46757.150228.9326
20.8617-0.19320.16141.3001-0.27141.30120.0055-0.1027-0.00970.0340.00330.033-0.00380.0327-0.00870.01560.0005-0.00510.08220.01390.0061-30.85518.753811.458
32.24710.16660.68351.20910.18042.05440.00370.2218-0.1198-0.18150.0305-0.10280.10450.2629-0.03420.09790.0187-0.00570.0976-0.02270.0221-29.715713.1525-16.6099
40.7859-0.27350.52421.11750.00512.6460.00110.12560.0173-0.19390.0192-0.0327-0.11840.0839-0.02030.0696-0.001-0.02050.0751-0.01020.0251-36.69519.9588-14.1759
59.64831.8812-3.964918.8799-1.40178.7221-0.12880.3256-0.4696-0.53680.07890.4120.5499-0.29840.04980.13790.0128-0.05490.081-0.010.1017-33.58690.3317-4.8287
61.06370.18420.31461.7934-0.01151.80580.03230.0449-0.0281-0.0833-0.0324-0.13320.04460.30480.00020.02040.01810.0030.14170.01350.0373-18.400515.42372.2699
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 7
2X-RAY DIFFRACTION2A8 - 149
3X-RAY DIFFRACTION3A150 - 222
4X-RAY DIFFRACTION4A223 - 279
5X-RAY DIFFRACTION5A280 - 285
6X-RAY DIFFRACTION6A286 - 321

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