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- PDB-8bb8: Crystal structure of human aldehyde dehydrogenase ALDH3A1 in comp... -

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Basic information

Entry
Database: PDB / ID: 8bb8
TitleCrystal structure of human aldehyde dehydrogenase ALDH3A1 in complex with octanal
ComponentsAldehyde dehydrogenase, dimeric NADP-preferring
KeywordsOXIDOREDUCTASE / aldehyde dehydrogenase / ALDH3A1 / odorant
Function / homology
Function and homology information


aldehyde dehydrogenase [NAD(P)+] / 3-chloroallyl aldehyde dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) activity / alcohol dehydrogenase (NADP+) activity / aldehyde dehydrogenase [NAD(P)+] activity / aldehyde metabolic process / aldehyde dehydrogenase (NAD+) activity / Phase I - Functionalization of compounds / xenobiotic metabolic process / lipid metabolic process ...aldehyde dehydrogenase [NAD(P)+] / 3-chloroallyl aldehyde dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) activity / alcohol dehydrogenase (NADP+) activity / aldehyde dehydrogenase [NAD(P)+] activity / aldehyde metabolic process / aldehyde dehydrogenase (NAD+) activity / Phase I - Functionalization of compounds / xenobiotic metabolic process / lipid metabolic process / endoplasmic reticulum / extracellular space / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Aldehyde dehydrogenase NAD(P)-dependent / 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, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
ACETATE ION / : / OCTANAL / Aldehyde dehydrogenase, dimeric NADP-preferring
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSchwartz, M. / Neiers, F.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: Sci Rep / Year: 2023
Title: Characterization of human oxidoreductases involved in aldehyde odorant metabolism.
Authors: Boichot, V. / Menetrier, F. / Saliou, J.M. / Lirussi, F. / Canon, F. / Folia, M. / Heydel, J.M. / Hummel, T. / Menzel, S. / Steinke, M. / Hackenberg, S. / Schwartz, M. / Neiers, F.
History
DepositionOct 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldehyde dehydrogenase, dimeric NADP-preferring
B: Aldehyde dehydrogenase, dimeric NADP-preferring
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,80211
Polymers104,1792
Non-polymers6239
Water15,457858
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10450 Å2
ΔGint-24 kcal/mol
Surface area32260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.341, 85.821, 169.209
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Aldehyde dehydrogenase, dimeric NADP-preferring / ALDHIII / Aldehyde dehydrogenase 3 / Aldehyde dehydrogenase family 3 member A1


Mass: 52089.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH3A1, ALDH3 / Production host: Escherichia coli (E. coli)
References: UniProt: P30838, aldehyde dehydrogenase [NAD(P)+]

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Non-polymers , 5 types, 867 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-OYA / OCTANAL / OCTYL ALDEHYDE


Mass: 128.212 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16O
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 858 / 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: 2.14 Å3/Da / Density % sol: 42.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 18 % PEG 3350, in 0.1 M potassium acetate pH 7.5 buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 1.8→49.66 Å / Num. obs: 82079 / % possible obs: 97.6 % / Redundancy: 12.6 % / Biso Wilson estimate: 22.85 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.318 / Rpim(I) all: 0.091 / Rrim(I) all: 0.331 / Net I/σ(I): 8.8
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3334 / CC1/2: 0.541 / Rpim(I) all: 0.632 / % possible all: 74.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SZA

3sza


Resolution: 1.8→49.66 Å / SU ML: 0.2112 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1454
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2276 4144 5.06 %
Rwork0.1802 77777 -
obs0.1826 81921 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.32 Å2
Refinement stepCycle: LAST / Resolution: 1.8→49.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6987 0 36 858 7881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00677196
X-RAY DIFFRACTIONf_angle_d0.82089742
X-RAY DIFFRACTIONf_chiral_restr0.05091089
X-RAY DIFFRACTIONf_plane_restr0.00611261
X-RAY DIFFRACTIONf_dihedral_angle_d13.14952729
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.31171100.29571802X-RAY DIFFRACTION69.2
1.82-1.840.3111150.28162188X-RAY DIFFRACTION83.53
1.84-1.860.3091250.26332325X-RAY DIFFRACTION88.03
1.86-1.880.30031420.2462374X-RAY DIFFRACTION92.03
1.88-1.910.3421240.23242480X-RAY DIFFRACTION94.11
1.91-1.940.25781540.22082582X-RAY DIFFRACTION98.77
1.94-1.960.26891300.20642632X-RAY DIFFRACTION99.5
1.96-1.990.28351610.20062622X-RAY DIFFRACTION99.93
1.99-2.020.24951260.2022625X-RAY DIFFRACTION99.96
2.02-2.060.22361220.20712644X-RAY DIFFRACTION99.86
2.06-2.090.23151320.20492641X-RAY DIFFRACTION99.86
2.09-2.130.26051530.18592613X-RAY DIFFRACTION99.93
2.13-2.170.25361390.18512636X-RAY DIFFRACTION99.86
2.17-2.220.2311380.17922656X-RAY DIFFRACTION100
2.22-2.260.21241250.18062661X-RAY DIFFRACTION99.96
2.26-2.320.25521400.18792628X-RAY DIFFRACTION99.89
2.32-2.370.21231250.18912674X-RAY DIFFRACTION100
2.37-2.440.25731570.19482626X-RAY DIFFRACTION100
2.44-2.510.2331570.18372635X-RAY DIFFRACTION100
2.51-2.590.23411290.18322661X-RAY DIFFRACTION99.96
2.59-2.680.23581200.18792692X-RAY DIFFRACTION99.86
2.68-2.790.23511550.18092645X-RAY DIFFRACTION99.96
2.79-2.920.23151250.18122665X-RAY DIFFRACTION100
2.92-3.070.22261390.18692703X-RAY DIFFRACTION100
3.07-3.260.23171620.18012638X-RAY DIFFRACTION99.96
3.26-3.520.21211480.16892673X-RAY DIFFRACTION100
3.52-3.870.19381630.16042694X-RAY DIFFRACTION99.97
3.87-4.430.21421420.14382726X-RAY DIFFRACTION99.97
4.43-5.580.20881230.15352767X-RAY DIFFRACTION99.97
5.58-49.660.18361630.17052869X-RAY DIFFRACTION99.7

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