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- PDB-3sza: Crystal structure of human ALDH3A1 - apo form -

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Basic information

Entry
Database: PDB / ID: 3sza
TitleCrystal structure of human ALDH3A1 - apo form
ComponentsAldehyde dehydrogenase, dimeric NADP-preferring
KeywordsOXIDOREDUCTASE / ALDH / Rossmann Fold
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 / cytoplasm / cytosol
Similarity search - Function
Aldehyde dehydrogenase NAD(P)-dependent / 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 NAD(P)-dependent / 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, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / Aldehyde dehydrogenase, dimeric NADP-preferring
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsKhanna, M. / Hurley, T.D.
Citation
Journal: J.Biol.Chem. / Year: 2011
Title: Discovery of a novel class of covalent inhibitor for aldehyde dehydrogenases.
Authors: Khanna, M. / Chen, C.H. / Kimble-Hill, A. / Parajuli, B. / Perez-Miller, S. / Baskaran, S. / Kim, J. / Dria, K. / Vasiliou, V. / Mochly-Rosen, D. / Hurley, T.D.
#1: Journal: Biochem Pharmacol / Year: 2008
Title: A point mutation produced a class 3 aldehyde dehydrogenase with increased protective ability against the killing effect of cyclophosphamide.
Authors: Ho, K.K. / Mukhopadhyay, A. / Li, Y.F. / Mukhopadhyay, S. / Weiner, H.
#2: Journal: Nat.Struct.Mol.Biol. / Year: 1997
Title: The first structure of an aldehyde dehydrogenase reveals novel interactions between NAD and the Rossmann Fold
Authors: Liu, Z.J. / Sun, Y.J. / Rose, J. / Chung, Y.J. / Hsiao, C.D. / Chang, W.R. / Kuo, I. / Perozich, J. / Lindahl, R. / Hempel, J. / Wang, B.C.
History
DepositionJul 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Sep 13, 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: Aldehyde dehydrogenase, dimeric NADP-preferring
B: Aldehyde dehydrogenase, dimeric NADP-preferring
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,7668
Polymers104,4912
Non-polymers2746
Water19,5821087
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9480 Å2
ΔGint-35 kcal/mol
Surface area32940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.412, 86.080, 170.396
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 52245.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH3, ALDH3A1 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P30838, aldehyde dehydrogenase [NAD(P)+]
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1087 / 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: 2.16 Å3/Da / Density % sol: 42.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.2 M potassium acetate, 18% PEG 3350, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9869 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 6, 2009
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9869 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. obs: 146816 / % possible obs: 97.8 % / Observed criterion σ(I): 0.2 / Redundancy: 4.7 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.058 / Χ2: 0.997 / Net I/σ(I): 16.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.48-1.5140.32768851.045192.3
1.51-1.534.50.28171251.1195.9
1.53-1.564.70.24772541.08197.7
1.56-1.594.80.22272901.095198.6
1.59-1.634.80.19373821.049199.2
1.63-1.674.90.1773811.086199.3
1.67-1.714.90.14874180.984199.6
1.71-1.754.90.13174520.945199.5
1.75-1.814.90.11574201.022199.8
1.81-1.864.90.10374181.058199.9
1.86-1.9340.12170521.23194.6
1.93-2.014.90.08274870.7321100
2.01-2.150.06975140.9821100
2.1-2.2150.06174810.9721100
2.21-2.354.10.06663740.917184.8
2.35-2.5350.0675380.9061100
2.53-2.7950.06175640.939199.9
2.79-3.1950.04775880.931199.9
3.19-4.024.60.0473680.96196.3
4.02-504.70.03278250.993197.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1ad3

1ad3


Resolution: 1.48→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.2095 / WRfactor Rwork: 0.1845 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8941 / SU B: 1.054 / SU ML: 0.041 / SU R Cruickshank DPI: 0.07 / SU Rfree: 0.0693 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1868 7380 5 %RANDOM
Rwork0.1649 ---
obs0.166 146724 97.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 48.37 Å2 / Biso mean: 16.4802 Å2 / Biso min: 5.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å20 Å2
2--0.95 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.48→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7019 0 12 1087 8118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227343
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.9739960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.955902
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.45224.537324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.394151337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4541543
X-RAY DIFFRACTIONr_chiral_restr0.1010.21137
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215471
X-RAY DIFFRACTIONr_mcbond_it0.8981.54537
X-RAY DIFFRACTIONr_mcangle_it1.61127395
X-RAY DIFFRACTIONr_scbond_it2.66832806
X-RAY DIFFRACTIONr_scangle_it4.4534.52564
LS refinement shellResolution: 1.481→1.52 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 507 -
Rwork0.23 9405 -
all-9912 -
obs-9405 89.91 %

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