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- PDB-3inl: Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2... -

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Basic information

Entry
Database: PDB / ID: 3inl
TitleHuman Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, complexed with agonist Alda-1
ComponentsAldehyde dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE / ALDH / E487K / Rossmann fold / Alda-1 / activator / Mitochondrion / NAD / Transit peptide
Function / homology
Function and homology information


Metabolism of serotonin / nitroglycerin reductase activity / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / phenylacetaldehyde dehydrogenase activity / aldehyde catabolic process / alcohol metabolic process / aldehyde dehydrogenase [NAD(P)+] activity / ethanol catabolic process / Ethanol oxidation ...Metabolism of serotonin / nitroglycerin reductase activity / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / phenylacetaldehyde dehydrogenase activity / aldehyde catabolic process / alcohol metabolic process / aldehyde dehydrogenase [NAD(P)+] activity / ethanol catabolic process / Ethanol oxidation / carboxylesterase activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / aldehyde dehydrogenase (NAD+) activity / Smooth Muscle Contraction / NAD binding / electron transfer activity / carbohydrate metabolic process / mitochondrial matrix / mitochondrion / extracellular exosome
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
Chem-BXB / Aldehyde dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.862 Å
AuthorsPerez-Miller, S. / Hurley, T.D.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Alda-1 is an agonist and chemical chaperone for the common human aldehyde dehydrogenase 2 variant.
Authors: Perez-Miller, S. / Younus, H. / Vanam, R. / Chen, C.H. / Mochly-Rosen, D. / Hurley, T.D.
#1: Journal: Science / Year: 2008
Title: Activation of Aldehyde Dehydrogenase-2 Reduces Ischemic Damage to the Heart
Authors: Chen, C.H. / Budas, G.R. / Churchill, E.N. / Disatnik, M.H. / Hurley, T.D. / Mochly-Rosen, D.
History
DepositionAug 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldehyde dehydrogenase, mitochondrial
B: Aldehyde dehydrogenase, mitochondrial
C: Aldehyde dehydrogenase, mitochondrial
D: Aldehyde dehydrogenase, mitochondrial
E: Aldehyde dehydrogenase, mitochondrial
F: Aldehyde dehydrogenase, mitochondrial
G: Aldehyde dehydrogenase, mitochondrial
H: Aldehyde dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)440,57055
Polymers435,8698
Non-polymers4,70147
Water61,3953408
1
A: Aldehyde dehydrogenase, mitochondrial
B: Aldehyde dehydrogenase, mitochondrial
C: Aldehyde dehydrogenase, mitochondrial
D: Aldehyde dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,25427
Polymers217,9354
Non-polymers2,32023
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24080 Å2
ΔGint-73 kcal/mol
Surface area59370 Å2
MethodPISA
2
E: Aldehyde dehydrogenase, mitochondrial
F: Aldehyde dehydrogenase, mitochondrial
G: Aldehyde dehydrogenase, mitochondrial
H: Aldehyde dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,31628
Polymers217,9354
Non-polymers2,38224
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23300 Å2
ΔGint-85 kcal/mol
Surface area59060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.121, 176.900, 102.323
Angle α, β, γ (deg.)90.000, 94.570, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Aldehyde dehydrogenase, mitochondrial / / ALDH class 2 / ALDHI / ALDH-E2


Mass: 54483.633 Da / Num. of mol.: 8 / Mutation: E487K, C302S
Source method: isolated from a genetically manipulated source
Details: lacks mitochondrial leader sequence / Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH2, ALDM / Plasmid: pT-7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05091, aldehyde dehydrogenase (NAD+)
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-BXB / N-(1,3-benzodioxol-5-ylmethyl)-2,6-dichlorobenzamide


Mass: 324.159 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C15H11Cl2NO3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3408 / 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: 2.11 Å3/Da / Density % sol: 41.81 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 6.4
Details: 100 MM ACES (N-[2-ACETAMIDO]-2-AMINOETHANE SULFONIC ACID), 10MM MGCL2, 100 MM GUANIDINE HCL, 16-17% W/V PEG 6000, 8MM DTT, pH 6.4, VAPOR DIFFUSION, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.07 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 20, 2009
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
Reflection twinOperator: l,-k,h / Fraction: 0.378
ReflectionResolution: 1.86→50 Å / Num. obs: 299181 / % possible obs: 98.7 % / Observed criterion σ(I): 0.2 / Redundancy: 3.7 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.09 / Χ2: 1.051 / Net I/σ(I): 14
Reflection shellResolution: 1.86→1.89 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 2.2 / Num. unique all: 11356 / Χ2: 1.047 / % possible all: 75.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
PHENIX1.4_4refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.862→49.003 Å / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0.09 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.168 1999 6.8 %In phenix, using lattice symmetry
Rwork0.136 ---
obs0.136 293169 97.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.433 Å2 / ksol: 0.314 e/Å3
Displacement parametersBiso max: 76.34 Å2 / Biso mean: 32.882 Å2 / Biso min: 20.4 Å2
Baniso -1Baniso -2Baniso -3
1--11.409 Å2-0 Å21.602 Å2
2---16.873 Å20 Å2
3----12.166 Å2
Refinement stepCycle: LAST / Resolution: 1.862→49.003 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30402 0 300 3408 34110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00531433
X-RAY DIFFRACTIONf_angle_d0.90642533
X-RAY DIFFRACTIONf_chiral_restr0.0554641
X-RAY DIFFRACTIONf_plane_restr0.0035570
X-RAY DIFFRACTIONf_dihedral_angle_d17.24511252
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.864-1.910.2171200.2217886180061800684
1.91-1.9620.2181360.198199792011593
1.962-2.020.2271410.181202892043095
2.02-2.0850.2161080.174207762088497
2.085-2.1590.1771540.169207672092197
2.159-2.2460.1771330.16210692120298
2.246-2.3480.2081430.153211062124999
2.348-2.4720.2181520.153211812133399
2.472-2.6260.1661420.147212552139799
2.626-2.8290.1881480.144212722142099
2.829-3.1140.1461560.129212772143399
3.114-3.5640.1341350.106213532148899
3.564-4.4890.1291470.089213592150699
4.489-38.1170.1441420.117215452168799

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