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- PDB-1ad3: CLASS 3 ALDEHYDE DEHYDROGENASE COMPLEX WITH NICOTINAMIDE-ADENINE-... -

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Basic information

Entry
Database: PDB / ID: 1ad3
TitleCLASS 3 ALDEHYDE DEHYDROGENASE COMPLEX WITH NICOTINAMIDE-ADENINE-DINUCLEOTIDE
ComponentsALDEHYDE DEHYDROGENASE (CLASS 3)
KeywordsOXIDOREDUCTASE / NADP / AROMATIC ALDEHYDE
Function / homology
Function and homology information


aldehyde dehydrogenase [NAD(P)+] / Phase I - Functionalization of compounds / 3-chloroallyl aldehyde dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) activity / alcohol dehydrogenase (NADP+) activity / aldehyde metabolic process / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / aldehyde dehydrogenase (NAD+) activity / response to cAMP / response to nutrient ...aldehyde dehydrogenase [NAD(P)+] / Phase I - Functionalization of compounds / 3-chloroallyl aldehyde dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) activity / alcohol dehydrogenase (NADP+) activity / aldehyde metabolic process / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / aldehyde dehydrogenase (NAD+) activity / response to cAMP / response to nutrient / response to glucocorticoid / lipid metabolic process / response to hypoxia / response to xenobiotic stimulus / positive regulation of cell population proliferation / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Aldehyde dehydrogenase, dimeric NADP-preferring
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / ISIRAS / Resolution: 2.6 Å
AuthorsLiu, Z.-J. / Rose, J. / Wang, B.C.
Citation
Journal: Nat.Struct.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.
#1: Journal: Enzymology and Molecular Biology of Carbonyl Metabolism 6 (in: Adv.Exp. Med.Biol., V.414)
Year: 1997
Title: Crystal Structure of a Class 3 Aldehyde Dehydrogenase at 2.6 Angstroms Resolution
Authors: Liu, Z.-J. / Hempel, J. / Sun, J. / Rose, J. / Hsiao, D. / Chang, W.-R. / Chung, Y.-J. / Kuo, I. / Lindahl, R. / Wang, B.-C.
#2: Journal: Enzymology and Molecular Biology of Carbonyl Metabolism 6 (in: Adv.Exp. Med.Biol., V.414)
Year: 1997
Title: Conserved Residues in the Aldehyde Dehydrogenase Family
Authors: Hempel, J. / Liu, Z.-J. / Perozich, J. / Rose, J. / Lindahl, R. / Wang, B.-C.
#3: Journal: Proteins / Year: 1990
Title: Preliminary Crystallographic Analysis of Class 3 Rat Liver Aldehyde Dehydrogenase
Authors: Rose, J.P. / Hempel, J. / Kuo, I. / Lindahl, R. / Wang, B.C.
History
DepositionJun 25, 1996Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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

Downloads & links

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Assembly

Deposited unit
A: ALDEHYDE DEHYDROGENASE (CLASS 3)
B: ALDEHYDE DEHYDROGENASE (CLASS 3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,9544
Polymers100,6272
Non-polymers1,3272
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10170 Å2
ΔGint-43 kcal/mol
Surface area31370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.950, 170.950, 47.160
Angle α, β, γ (deg.)90.00, 110.25, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.1895, 0.0654, -0.9797), (0.0639, -0.9948, -0.0787), (-0.9798, -0.0776, 0.1843)
Vector: 85.5899, 101.2096, 77.5218)
DetailsALDEHYDE DEHYDROGENASE IS A HOMODIMER. THE FULL DIMER IS PRESENT IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT.

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Components

#1: Protein ALDEHYDE DEHYDROGENASE (CLASS 3) / ALDH


Mass: 50313.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: LIVER / Plasmid: PTA1DH / Production host: Escherichia coli (E. coli) / Strain (production host): BH101
References: UniProt: P11883, aldehyde dehydrogenase [NAD(P)+]
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.45 Å3/Da / Density % sol: 50 %
Crystal growpH: 6.2 / Details: pH 6.2
Crystal grow
*PLUS
Method: vapor diffusion
Details: Rose, J.P., (1990) Proteins: Struct.,Funct., Genet., 8, 305.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.7 mg/mlprotein1drop
21.5 %(w/v)PEG80001drop
30.05 %(w/v)mercaptoethanol1drop
40.5 mMEDTA1drop
50.25 mg/mlNAD1drop
612.5 mMPIPES1drop
70.05 %(w/v)mercaptoethanol1reservoir
80.5 mMEDTA1reservoir
90.25 mg/mlNAD1reservoir
1012.5 mMPIPES1reservoir
112.5 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jun 1, 1994 / Details: SUPPER MIRRORS (SMALL)
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.5 Å / Num. obs: 25656 / % possible obs: 80 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Biso Wilson estimate: 23.62 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.444
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 2.29 / % possible all: 50
Reflection shell
*PLUS
% possible obs: 50 %

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Processing

Software
NameVersionClassification
ISIRASmodel building
X-PLOR3.1refinement
XENGENV. 2.1data reduction
XENGENV. 2.1data scaling
ISIRASphasing
RefinementMethod to determine structure: ISIRAS / Resolution: 2.6→8 Å / Rfactor Rfree error: 0.006 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1914 8 %RANDOM
Rwork0.177 ---
obs0.177 22435 80 %-
Displacement parametersBiso mean: 18.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6964 0 88 284 7336
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.457
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.404
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.6→2.7 Å / Rfactor Rfree error: 0.031
RfactorNum. reflection% reflection
Rfree0.36 131 -
Rwork0.24 1464 -
obs--50 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.404

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