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- PDB-4wgg: STRUCTURE OF THE TERNARY COMPLEX OF A ZINGIBER OFFICINALE DOUBLE ... -

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Basic information

Entry
Database: PDB / ID: 4wgg
TitleSTRUCTURE OF THE TERNARY COMPLEX OF A ZINGIBER OFFICINALE DOUBLE BOND REDUCTASE IN COMPLEX WITH NADP AND CONIFERYL ALDEHYDE
ComponentsDouble Bond Reductase
KeywordsOXIDOREDUCTASE / ROSSMANN FOLD / TWISTED B-BARREL / CURCUMINOID REDUCTASE / PLANT PROTEIN
Function / homology
Function and homology information


2-alkenal reductase [NAD(P)+] activity / response to oxidative stress / nucleotide binding
Similarity search - Function
Medium-chain dehydrogenase/reductase / Oxidoreductase, N-terminal domain / N-terminal domain of oxidoreductase / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily ...Medium-chain dehydrogenase/reductase / Oxidoreductase, N-terminal domain / N-terminal domain of oxidoreductase / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / 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
(2E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enal / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Zingiber officinale double bond reductase
Similarity search - Component
Biological speciesZingiber officinale (ginger)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsCollery, J. / Langlois d'Estaintot, B. / Buratto, J. / Granier, T. / Gallois, B. / Willis, M.A. / Sang, Y. / Flores-Sanchez, I.J. / Gang, D.R.
CitationJournal: to be published
Title: STRUCTURE OF ZINGIBER OFFICINALE DOUBLE BOND REDUCTASE
Authors: Buratto, J. / Langlois d'Estaintot, B. / Granier, T. / Gallois, B. / Willis, M.A. / Sang, Y. / Flores-Sanchez, I.J. / Gang, D.R.
History
DepositionSep 18, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_PDB_remark / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name / _citation_author.name / _database_PDB_remark.text
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Double Bond Reductase
B: Double Bond Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4345
Polymers78,7692
Non-polymers1,6653
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-34 kcal/mol
Surface area27860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.748, 77.889, 155.882
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a dimer. There are 2 biological units in the asymmetric unit (chains A & B and chains C & D

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Components

#1: Protein Double Bond Reductase


Mass: 39384.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zingiber officinale (ginger) / Plasmid: pEXP5-CT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A096LNF0*PLUS
#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
#3: Chemical ChemComp-CIY / (2E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enal / Coniferaldehyde


Mass: 178.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O

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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: 2.34 Å3/Da / Density % sol: 47.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: PEG 1500 25%, PCB 100 mM, NaN3 3mM / PH range: 4.5 - 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: May 15, 2014 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20.95 Å / Num. all: 28133 / Num. obs: 26690 / % possible obs: 94.54 % / Redundancy: 2.1 % / Rsym value: 0.0753 / Net I/σ(I): 11.23
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 2.49 / % possible all: 92.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.339
Highest resolutionLowest resolution
Rotation20.36 Å2.54 Å

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
PDB_EXTRACT3.15data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NH4

4nh4


Resolution: 2.4→20.9 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.884 / WRfactor Rfree: 0.2448 / WRfactor Rwork: 0.1677 / FOM work R set: 0.8049 / SU R Cruickshank DPI: 0.6163 / SU Rfree: 0.3239 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.616 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2788 1422 5.1 %RANDOM
Rwork0.1897 26690 --
obs0.1942 26690 94.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.84 Å2 / Biso mean: 29.931 Å2 / Biso min: 8.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å2-0 Å20 Å2
2--0.77 Å2-0 Å2
3----1.45 Å2
Refinement stepCycle: final / Resolution: 2.4→20.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5361 0 109 332 5802
Biso mean--39.37 31.63 -
Num. residues----698
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.025628
X-RAY DIFFRACTIONr_angle_refined_deg1.7041.9837646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8335698
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.90324.103234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.19515892
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5931519
X-RAY DIFFRACTIONr_chiral_restr0.1040.2838
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214250
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 100 -
Rwork0.283 1858 -
all-1958 -
obs--90.73 %

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