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- PDB-4i8q: Structure of the aminoaldehyde dehydrogenase 1 E260A mutant from ... -

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Basic information

Entry
Database: PDB / ID: 4i8q
TitleStructure of the aminoaldehyde dehydrogenase 1 E260A mutant from Solanum lycopersicum (SlAMADH1-E260A)
ComponentsPutative betaine aldehyde dehyrogenase
KeywordsOXIDOREDUCTASE / AMADH10 family fold
Function / homology
Function and homology information


gamma-guanidinobutyraldehyde dehydrogenase / gamma-guanidinobutyraldehyde dehydrogenase activity / 4-trimethylammoniobutyraldehyde dehydrogenase / 4-trimethylammoniobutyraldehyde dehydrogenase activity / aminobutyraldehyde dehydrogenase / aminobutyraldehyde dehydrogenase activity / betaine-aldehyde dehydrogenase / betaine-aldehyde dehydrogenase activity / glycine betaine biosynthetic process from choline / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor ...gamma-guanidinobutyraldehyde dehydrogenase / gamma-guanidinobutyraldehyde dehydrogenase activity / 4-trimethylammoniobutyraldehyde dehydrogenase / 4-trimethylammoniobutyraldehyde dehydrogenase activity / aminobutyraldehyde dehydrogenase / aminobutyraldehyde dehydrogenase activity / betaine-aldehyde dehydrogenase / betaine-aldehyde dehydrogenase activity / glycine betaine biosynthetic process from choline / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / sodium ion binding / cellular detoxification of aldehyde / nucleotide binding / protein homodimerization activity
Similarity search - Function
Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family ...Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Aminoaldehyde dehydrogenase 1
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsMorera, S. / Vigouroux, A. / Kopecny, D.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Plant ALDH10 family: identifying critical residues for substrate specificity and trapping a thiohemiacetal intermediate.
Authors: Kopecny, D. / Koncitikova, R. / Tylichova, M. / Vigouroux, A. / Moskalikova, H. / Soural, M. / Sebela, M. / Morera, S.
History
DepositionDec 4, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 1, 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: Putative betaine aldehyde dehyrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,39613
Polymers55,9571
Non-polymers1,43912
Water1,74797
1
A: Putative betaine aldehyde dehyrogenase
hetero molecules

A: Putative betaine aldehyde dehyrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,79226
Polymers111,9142
Non-polymers2,87924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y+1/2,z1
Buried area12650 Å2
ΔGint-62 kcal/mol
Surface area34520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.040, 118.070, 128.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative betaine aldehyde dehyrogenase / Aminoaldehyde dehydrogenase 1


Mass: 55956.914 Da / Num. of mol.: 1 / Mutation: E260A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: Solyc06g071290.2 / Plasmid: pCDFDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 PlysS / References: UniProt: Q56R04

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Non-polymers , 5 types, 109 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 97 / 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: 3.32 Å3/Da / Density % sol: 62.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 1500, 100mM Imidazol, 10% glycerol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2012
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. all: 22000 / Num. obs: 21922 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Biso Wilson estimate: 57.82 Å2
Reflection shellResolution: 2.65→2.81 Å / % possible all: 98.5

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Processing

Software
NameVersionClassification
PX1data collection
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I9B

4i9b


Resolution: 2.65→28.77 Å / Cor.coef. Fo:Fc: 0.8854 / Cor.coef. Fo:Fc free: 0.8054 / SU R Cruickshank DPI: 0.448 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2821 1096 5 %RANDOM
Rwork0.2087 ---
all0.23 22000 --
obs0.2123 21906 99.73 %-
Displacement parametersBiso mean: 45.22 Å2
Baniso -1Baniso -2Baniso -3
1-12.5926 Å20 Å20 Å2
2---6.7386 Å20 Å2
3----5.854 Å2
Refine analyzeLuzzati coordinate error obs: 0.331 Å
Refinement stepCycle: LAST / Resolution: 2.65→28.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3779 0 94 97 3970
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013945HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.235338HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1366SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes87HARMONIC2
X-RAY DIFFRACTIONt_gen_planes580HARMONIC5
X-RAY DIFFRACTIONt_it3945HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.83
X-RAY DIFFRACTIONt_other_torsion21.09
X-RAY DIFFRACTIONt_chiral_improper_torsion529SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4697SEMIHARMONIC4
LS refinement shellResolution: 2.65→2.78 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2868 142 5.02 %
Rwork0.2195 2687 -
all0.2229 2829 -
obs--99.73 %

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