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- PDB-3n80: Human mitochondrial aldehyde dehydrogenase, apo form -

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Basic information

Entry
Database: PDB / ID: 3n80
TitleHuman mitochondrial aldehyde dehydrogenase, apo form
ComponentsAldehyde dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE / ALDH / Rossmann fold
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
GUANIDINE / Aldehyde dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Direct Refinement / Resolution: 1.5 Å
AuthorsGonzalez-Segura, L. / Hurley, T.D.
Citation
Journal: To be published
Title: Conformational Selection During Catalysis: The role of Threonine 244 in ALDH2
Authors: Ho, K.-K. / Gonzalez-Segura, L. / Perez-Miller, S. / Weiner, H. / Hurley, T.D.
#1: Journal: Biochemistry / Year: 2006
Title: Selective Alteration of the Rate-Limiting Step in Cytosolic Aldehyde Dehydrogenase through Random Mutagenesis
Authors: Ho, K.-K. / Hurley, T.D. / Weiner, H.
#2: Journal: J. Biol. Chem. / Year: 2007
Title: Structural and Functional Consequences of Coenzyme Binding to the Inactive Asian Variant of Mitochondrial Aldehyde Dehydrogenase (Roles of residues 475 and 487)
Authors: Larson, H.N. / Zhou, J. / Chen, Z. / Stamler, J.S. / Weiner, H. / Hurley, T.D.
History
DepositionMay 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Sep 6, 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 / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.pdbx_leaving_atom_flag / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)439,78573
Polymers436,1258
Non-polymers3,66065
Water88,0394887
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)219,83935
Polymers218,0634
Non-polymers1,77731
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26930 Å2
ΔGint-51 kcal/mol
Surface area58110 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)219,94638
Polymers218,0634
Non-polymers1,88334
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27400 Å2
ΔGint-59 kcal/mol
Surface area58330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.662, 152.291, 177.282
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

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


Mass: 54515.629 Da / Num. of mol.: 8 / Fragment: Mature sequence, residues 18-517
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+)

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Non-polymers , 5 types, 4952 molecules

#2: Chemical...
ChemComp-GAI / GUANIDINE / Guanidine


Mass: 59.070 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: CH5N3
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4887 / 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: 2.19 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 6.4
Details: 100 MM ACES (N-[2-ACETAMIDO]-2-AMINOETHANE SULFONIC ACID), 1-10MM MGCL2, 100-200 MM GUANIDINE HCL, 16-17% W/V PEG 6000, 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: 1.04 Å
DetectorType: APS-1 / Detector: CCD / Date: Oct 15, 2005
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 599824 / % possible obs: 98.9 % / Redundancy: 3.1 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 20.1
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-3000data reduction
HKL-3000data scaling
REFMACphasing
RefinementMethod to determine structure: Direct Refinement
Starting model: PDB Entry 1o05

1o05


Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 1.035 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.175 30068 5 %RANDOM
Rwork0.149 ---
obs0.151 599778 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 54.63 Å2 / Biso mean: 13.136 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2---0.16 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30401 0 236 4887 35524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02231945
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.95443399
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.6195.0774175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7424.7291440
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.776155206
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.46615162
X-RAY DIFFRACTIONr_chiral_restr0.1040.24752
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02124687
X-RAY DIFFRACTIONr_mcbond_it0.8471.520056
X-RAY DIFFRACTIONr_mcangle_it1.423232264
X-RAY DIFFRACTIONr_scbond_it2.492311889
X-RAY DIFFRACTIONr_scangle_it4.0744.511064
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 2225 -
Rwork0.178 42334 -
all-44559 -
obs-44559 99.92 %

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