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

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Basic information

Entry
Database: PDB / ID: 4idb
TitleStructure of the Fragaria x ananassa enone oxidoreductase in complex with NADP+
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
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: 1.55 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)36,4036
Polymers35,3771
Non-polymers1,0265
Water8,035446
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.258, 70.258, 174.799
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-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-SO4 / SULFATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 446 / 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: 3.05 Å3/Da / Density % sol: 59.65 %
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: 14.1 / 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: 1.55→30 Å / Num. all: 64320 / Num. obs: 64320 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 9.66 % / Biso Wilson estimate: 26.532 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 24.39
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
1.55-1.650.5320.7813.310574910833107740.82499.5
1.65-1.80.290.4255.9311855912110120730.44899.7
1.8-20.1270.18512.6610804411018109990.19599.8
2-30.0390.06133.3420441421142211390.065100
3-40.0140.02961.9948497527652760.031100
4-60.0090.02171.9225246279827950.02299.9
6-80.0090.01771.2762637167140.01899.7
8-100.0060.01472.3822192672650.01599.3
10-300.0060.01268.4421303082850.01392.5

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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: 1.55→29.59 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / WRfactor Rfree: 0.165 / WRfactor Rwork: 0.1398 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9142 / SU B: 1.912 / SU ML: 0.037 / SU R Cruickshank DPI: 0.0554 / SU Rfree: 0.0584 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1712 1953 3 %RANDOM
Rwork0.1463 ---
all0.147 64320 --
obs0.147 64320 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 150.08 Å2 / Biso mean: 24.4402 Å2 / Biso min: 11.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å2-0 Å2-0 Å2
2--0.28 Å2-0 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.55→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2405 0 65 446 2916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192560
X-RAY DIFFRACTIONr_bond_other_d0.0010.022504
X-RAY DIFFRACTIONr_angle_refined_deg1.9562.0223499
X-RAY DIFFRACTIONr_angle_other_deg0.8935810
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5245331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41125.11984
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.19115418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.683156
X-RAY DIFFRACTIONr_chiral_restr0.1250.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212810
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02493
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 136 -
Rwork0.211 4525 -
all-4661 -
obs--99.4 %
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)
123.8813-2.2911-15.51893.62660.83910.20870.516-1.22881.0587-0.02190.22720.2052-0.3480.7767-0.74321.8059-0.54420.15540.85590.14890.4699-35.43747.067728.8364
21.3824-0.51730.27192.3376-0.50021.59240.0183-0.16810.054-0.03030.02630.0399-0.04140.0354-0.04460.0051-0.0077-0.00460.08940.01270.0212-30.966820.161612.6175
32.4405-2.30342.99922.204-3.04675.59510.09-0.0527-0.2913-0.08890.04870.2390.23480.0238-0.13860.09690.0137-0.03260.0462-0.0040.0853-33.201610.7349-1.3195
43.3990.77121.07541.27130.26272.8810.01860.2512-0.1109-0.25570.0598-0.19290.1550.513-0.07840.12730.0389-0.00390.1528-0.05070.0716-28.245312.7815-17.6677
51.89780.54762.52012.74492.28588.3925-0.13330.29510.1861-0.43070.223-0.2078-0.44950.5993-0.08970.1304-0.02670.00350.12060.00310.0624-34.626422.573-20.6631
61.1554-0.50420.58360.9031-0.46041.41570.07690.0466-0.08-0.2377-0.0588-0.04760.15430.2115-0.01820.0920.01310.00490.1003-0.00390.0428-27.34514.4737-0.9903
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 7
2X-RAY DIFFRACTION2A8 - 133
3X-RAY DIFFRACTION3A134 - 158
4X-RAY DIFFRACTION4A159 - 222
5X-RAY DIFFRACTION5A223 - 256
6X-RAY DIFFRACTION6A257 - 321

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