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

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Basic information

Entry
Database: PDB / ID: 6ysb
TitleCrystal structure of Malus domestica Double Bond Reductase (MdDBR) apo form
Components2-alkenal reductase (NADP(+)-dependent)-like
KeywordsBIOSYNTHETIC PROTEIN / phenylpropanoid pathway / double bond reductase / Malus domestica
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
Similarity search - Function
Oxidoreductase, N-terminal domain / Medium-chain dehydrogenase/reductase / N-terminal domain of oxidoreductase / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
2-alkenal reductase (NADP(+)-dependent)-like
Similarity search - Component
Biological speciesPyrus ussuriensis x Pyrus communis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 21, 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
B: 2-alkenal reductase (NADP(+)-dependent)-like
A: 2-alkenal reductase (NADP(+)-dependent)-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1674
Polymers76,9752
Non-polymers1922
Water9,494527
1
B: 2-alkenal reductase (NADP(+)-dependent)-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5832
Polymers38,4871
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 2-alkenal reductase (NADP(+)-dependent)-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5832
Polymers38,4871
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.609, 68.666, 68.944
Angle α, β, γ (deg.)90.000, 111.380, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 2-alkenal reductase (NADP(+)-dependent)-like


Mass: 38487.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrus ussuriensis x Pyrus communis (plant)
Gene: D8674_014777 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5N5GUE7*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / Source method: isolated from a natural source / Formula: H2O
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: 2.24 Å3/Da / Density % sol: 45.14 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
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 PILATUS3 S 2M / Detector: PIXEL / Date: Jun 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→48.72 Å / Num. obs: 210636 / % possible obs: 99.4 % / Redundancy: 3.6 % / CC1/2: 0.998 / Net I/σ(I): 12.1
Reflection shellResolution: 1.2→1.22 Å / Num. unique obs: 10469 / CC1/2: 0.784

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J3H

2j3h


Resolution: 1.2→48.62 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.381 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.041
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1975 10528 5 %RANDOM
Rwork0.1615 ---
obs0.1633 200156 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 223.06 Å2 / Biso mean: 24.003 Å2 / Biso min: 11.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å2-0 Å20.72 Å2
2---0.91 Å20 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.2→48.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5261 0 10 527 5798
Biso mean--23.83 31.71 -
Num. residues----678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0135379
X-RAY DIFFRACTIONr_bond_other_d0.0040.0175123
X-RAY DIFFRACTIONr_angle_refined_deg2.1261.647257
X-RAY DIFFRACTIONr_angle_other_deg1.6011.57711906
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0185674
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24323.22236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70215955
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2911520
X-RAY DIFFRACTIONr_chiral_restr0.1230.2670
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025938
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021091
X-RAY DIFFRACTIONr_rigid_bond_restr11.434310497
LS refinement shellResolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 734 -
Rwork0.239 14893 -
all-15627 -
obs--99.84 %

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