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- PDB-6ytz: Crystal structure of Malus domestica Double Bond Reductase (MdDBR... -

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Basic information

Entry
Database: PDB / ID: 6ytz
TitleCrystal structure of Malus domestica Double Bond Reductase (MdDBR) in complex with NADPH
ComponentsDouble Bond Reductase
KeywordsBIOSYNTHETIC PROTEIN / phenylpropanoid pathway / double bond reductase / Malus domestica
Function / homologyNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / R-1,2-PROPANEDIOL
Function and homology information
Biological speciesMalus domestica (apple)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsCaliandro, R. / Polsinelli, I. / Demitri, N. / Benini, S.
CitationJournal: Int.J.Biol.Macromol. / Year: 2021
Title: The structural and functional characterization of Malus domestica double bond reductase MdDBR provides insights towards the identification of its substrates.
Authors: Caliandro, R. / Polsinelli, I. / Demitri, N. / Musiani, F. / Martens, S. / Benini, S.
History
DepositionApr 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5076
Polymers38,4841
Non-polymers1,0235
Water5,170287
1
A: Double Bond Reductase
hetero molecules

A: Double Bond Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,01412
Polymers76,9692
Non-polymers2,04510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area7070 Å2
ΔGint-68 kcal/mol
Surface area28650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.545, 68.645, 145.398
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-564-

HOH

21A-752-

HOH

31A-783-

HOH

41A-785-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Double Bond Reductase


Mass: 38484.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Malus domestica (apple) / Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 292 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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PGR / R-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.21 Å3/Da / Density % sol: 44.23 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.03 M magnesium chloride, 0.03 M calcium chloride, 0.03 M sodium chloride, 0.03 M sodium bromide, 0.03 M sodium iodide in 0.1 M MES/imidazole pH 6.5.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→48.5 Å / Num. obs: 67744 / % possible obs: 100 % / Redundancy: 12.47 % / CC1/2: 1 / Net I/σ(I): 15.9
Reflection shellResolution: 1.4→1.42 Å / Num. unique obs: 3301 / CC1/2: 0.517

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
MOLREPphasing
PDB_EXTRACT3.25data extraction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YSB

6ysb


Resolution: 1.4→48.44 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.976 / SU B: 2.277 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1661 3403 5 %RANDOM
Rwork0.1215 ---
obs0.1237 64352 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 133.2 Å2 / Biso mean: 25.337 Å2 / Biso min: 13.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å2-0 Å20 Å2
2---0.14 Å2-0 Å2
3---0.51 Å2
Refinement stepCycle: final / Resolution: 1.4→48.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2703 0 66 288 3057
Biso mean--24.67 39.59 -
Num. residues----351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0132857
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172713
X-RAY DIFFRACTIONr_angle_refined_deg1.9191.6453875
X-RAY DIFFRACTIONr_angle_other_deg1.5191.5756305
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.245361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71323.193119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.99115494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5571510
X-RAY DIFFRACTIONr_chiral_restr0.1160.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023158
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02575
X-RAY DIFFRACTIONr_rigid_bond_restr4.19135566
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 284 -
Rwork0.383 4669 -
all-4953 -
obs--100 %

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