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- PDB-2ono: Arg475Gln Mutant of Mitochondrial Aldehyde Dehydrogenase, apo for... -

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Basic information

Entry
Database: PDB / ID: 2ono
TitleArg475Gln Mutant of Mitochondrial Aldehyde Dehydrogenase, apo form, pseudo-merohedrally twinned
ComponentsAldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / ALDH / NAD / Rossmann Fold
Function / homology
Function and homology information


Metabolism of serotonin / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / phenylacetaldehyde dehydrogenase (NAD+) activity / nitroglycerin metabolic process / aldehyde catabolic process / alcohol metabolic process / aldehyde dehydrogenase [NAD(P)+] activity / ethanol catabolic process / Ethanol oxidation ...Metabolism of serotonin / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / phenylacetaldehyde dehydrogenase (NAD+) activity / nitroglycerin metabolic process / aldehyde catabolic process / alcohol metabolic process / aldehyde dehydrogenase [NAD(P)+] activity / ethanol catabolic process / Ethanol oxidation / aldehyde dehydrogenase (NAD+) / carboxylesterase activity / aldehyde dehydrogenase (NAD+) activity / Smooth Muscle Contraction / Mitochondrial protein degradation / NAD binding / carbohydrate metabolic process / electron transfer activity / 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, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Aldehyde dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsLarson, H.N. / Hurley, T.D.
CitationJournal: 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
DepositionJan 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 2023Group: 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

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Assembly

Deposited unit
A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
C: Aldehyde dehydrogenase
D: Aldehyde dehydrogenase
E: Aldehyde dehydrogenase
F: Aldehyde dehydrogenase
G: Aldehyde dehydrogenase
H: Aldehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)435,7648
Polymers435,7648
Non-polymers00
Water18,3751020
1
A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
C: Aldehyde dehydrogenase
D: Aldehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)217,8824
Polymers217,8824
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20020 Å2
ΔGint-63 kcal/mol
Surface area59050 Å2
MethodPISA
2
E: Aldehyde dehydrogenase
F: Aldehyde dehydrogenase
G: Aldehyde dehydrogenase
H: Aldehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)217,8824
Polymers217,8824
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20170 Å2
ΔGint-65 kcal/mol
Surface area58890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.472, 175.850, 101.458
Angle α, β, γ (deg.)90.00, 94.79, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a tetramer. There are 3 biological untils in the assymmetric unit. The biological unit 1 consists of chain(s) A, B, C, D. The biological unit 2 consists of chain(s) E, F, G, H.

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Components

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


Mass: 54470.562 Da / Num. of mol.: 8 / Mutation: R475Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH2, ALDM / Plasmid: pT-7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P05091, aldehyde dehydrogenase (NAD+)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1020 / 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: 2.069 Å3/Da / Density % sol: 41.15 %
Crystal growTemperature: 293 K / pH: 6.6
Details: 100 mM ACES (N-[2-Acetamido]-2-aminoethane sufonic acid), 5 mM MgCl2, 100 mM Guanidine HCl, 18% w/v PEG 6000, 6 mM DTT, pH 6.6, vapor diffusion, temperature 293K, pH 6.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 3, 2003
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.15→25 Å / Num. obs: 186854 / % possible obs: 97.5 % / Observed criterion σ(I): 0.2 / Biso Wilson estimate: 21.84 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.6
Reflection shellResolution: 2.15→2.23 Å / Rmerge(I) obs: 0.198 / % possible all: 87.8

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Processing

Software
NameClassification
DENZOdata reduction
AMoREphasing
SHELXL-97refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O05

1o05


Resolution: 2.15→10 Å / Num. parameters: 125536 / Num. restraintsaints: 316424 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.314 8781 -RANDOM
all0.251 180487 --
obs0.251 175614 92.5 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 31383
Refinement stepCycle: LAST / Resolution: 2.15→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30368 0 0 1020 31388
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.013
X-RAY DIFFRACTIONs_similar_dist0.036
X-RAY DIFFRACTIONs_from_restr_planes0.019
X-RAY DIFFRACTIONs_zero_chiral_vol0.006
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.013
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.031
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.027
X-RAY DIFFRACTIONs_approx_iso_adps0

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