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- PDB-8con: Crystal structure of alcohol dehydrogenase from Arabidopsis thali... -

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Basic information

Entry
Database: PDB / ID: 8con
TitleCrystal structure of alcohol dehydrogenase from Arabidopsis thaliana in complex with NADH
ComponentsAlcohol dehydrogenase class-P
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase / Zn-binding dehydrogenase / metalloprotein / Rossman fold
Function / homology
Function and homology information


response to flooding / positive regulation of cellular response to hypoxia / response to sucrose / alcohol dehydrogenase (NAD+) activity / response to water deprivation / response to abscisic acid / alcohol dehydrogenase / response to caffeine / response to osmotic stress / response to salt stress ...response to flooding / positive regulation of cellular response to hypoxia / response to sucrose / alcohol dehydrogenase (NAD+) activity / response to water deprivation / response to abscisic acid / alcohol dehydrogenase / response to caffeine / response to osmotic stress / response to salt stress / response to cold / response to hydrogen peroxide / response to estradiol / cellular response to hypoxia / response to hypoxia / nucleotide binding / protein homodimerization activity / zinc ion binding / plasma membrane / cytosol
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Alcohol dehydrogenase class-P
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFermani, S. / Fanti, S. / Carloni, G. / Falini, G. / Meloni, M. / Zaffagnini, M.
Funding support Italy, 1items
OrganizationGrant numberCountry
Not funded Italy
CitationJournal: Plant J. / Year: 2024
Title: Structural and biochemical characterization of Arabidopsis alcohol dehydrogenases reveals distinct functional properties but similar redox sensitivity.
Authors: Meloni, M. / Rossi, J. / Fanti, S. / Carloni, G. / Tedesco, D. / Treffon, P. / Piccinini, L. / Falini, G. / Trost, P. / Vierling, E. / Licausi, F. / Giuntoli, B. / Musiani, F. / Fermani, S. / Zaffagnini, M.
History
DepositionFeb 28, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alcohol dehydrogenase class-P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,84920
Polymers41,2291
Non-polymers2,62019
Water4,486249
1
A: Alcohol dehydrogenase class-P
hetero molecules

A: Alcohol dehydrogenase class-P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,69840
Polymers82,4582
Non-polymers5,24038
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area14190 Å2
ΔGint-131 kcal/mol
Surface area27950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.405, 63.405, 182.153
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-406-

SO4

21A-711-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alcohol dehydrogenase class-P / AtADH


Mass: 41229.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ADH1, ADH, At1g77120, F22K20.19 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / References: UniProt: P06525, alcohol dehydrogenase

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Non-polymers , 7 types, 268 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.57 Å3/Da / Density % sol: 52 % / Description: bipyramidal or or rhombohedral
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Hepes-NaOH pH 7.0-8.0, 2% v/v PEG 400 and 2.0 M (NH4)2SO4
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2021
RadiationMonochromator: Double Crystal Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→182.15 Å / Num. obs: 47829 / % possible obs: 100 % / Redundancy: 8.5 % / Biso Wilson estimate: 24.07 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.035 / Rrim(I) all: 0.076 / Net I/σ(I): 15.1
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.711 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2492 / CC1/2: 0.827 / Rpim(I) all: 0.411 / Rrim(I) all: 0.826 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→47.02 Å / SU ML: 0.192 / Cross valid method: FREE R-VALUE / σ(F): 0.1
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.214 4495 4.99 %RANDOM SELECTION
Rwork0.186 ---
obs0.187 47747 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.77 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2889 0 160 249 3298
LS refinement shellResolution: 1.7→1.72 Å
RfactorNum. reflection% reflection
Rfree0.2707 100 -
Rwork0.2778 3004 -
obs--99.65 %

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