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- PDB-8dr9: Crystal structure of human ALDH2 in complex with NAD+ and PEG MME 550 -

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Basic information

Entry
Database: PDB / ID: 8dr9
TitleCrystal structure of human ALDH2 in complex with NAD+ and PEG MME 550
ComponentsAldehyde dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE / ALDH2 / aldehyde dehydrogenase / mitochondrial
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, 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
Similarity search - Domain/homology
CITRIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Aldehyde dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsXu, S.Y. / Weng, J.K.
Funding support United States, 1items
OrganizationGrant numberCountry
W. M. Keck Foundation United States
CitationJournal: To be published
Title: Crystal structure of human ALDH2 in complex with NAD+ and PEG MME 550
Authors: Xu, S.Y. / Weng, J.K.
History
DepositionJul 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aldehyde dehydrogenase, mitochondrial
B: Aldehyde dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,98317
Polymers109,0812
Non-polymers3,90215
Water16,952941
1
A: Aldehyde dehydrogenase, mitochondrial
B: Aldehyde dehydrogenase, mitochondrial
hetero molecules

A: Aldehyde dehydrogenase, mitochondrial
B: Aldehyde dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,96634
Polymers218,1624
Non-polymers7,80330
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Unit cell
Length a, b, c (Å)119.961, 119.961, 135.287
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-1094-

HOH

21A-1103-

HOH

31B-1078-

HOH

41B-1087-

HOH

51B-1097-

HOH

61B-1144-

HOH

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 54540.621 Da / Num. of mol.: 2 / Mutation: C302S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH2, ALDM / Plasmid: pHIS8-4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P05091, aldehyde dehydrogenase (NAD+)

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Non-polymers , 5 types, 956 molecules

#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H22O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 941 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.23 Å3/Da / Density % sol: 44.94 % / Description: 3D
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: protein conditions: 8 mg/ml recombinant ALDH2 in 20 mM Tris-HCl, pH 8.0, 50 mM NaCl, 1 mM DTT, supplemented with 2-4% v/v DMSO well conditions: 100 mM sodium citrate, pH 5.0-5.6, 22-26% w/v ...Details: protein conditions: 8 mg/ml recombinant ALDH2 in 20 mM Tris-HCl, pH 8.0, 50 mM NaCl, 1 mM DTT, supplemented with 2-4% v/v DMSO well conditions: 100 mM sodium citrate, pH 5.0-5.6, 22-26% w/v PEG MME 550 550 hanging drops were set with a 1.5:1 protein:well ratio
PH range: 5.0-5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.984 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.5→49.92 Å / Num. obs: 155768 / % possible obs: 99.9 % / Redundancy: 13.5 % / CC1/2: 0.999 / Net I/σ(I): 16.37
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 13.7 % / Num. unique obs: 24827 / CC1/2: 0.809 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
REFMAC5.8.0352refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VLE

2vle


Resolution: 1.5→49.92 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.111 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1574 7832 5 %RANDOM
Rwork0.1358 ---
obs0.1369 147935 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.33 Å2 / Biso mean: 15.868 Å2 / Biso min: 4.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å2-0 Å2-0 Å2
2--0.47 Å2-0 Å2
3----0.94 Å2
Refinement stepCycle: final / Resolution: 1.5→49.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7600 0 280 941 8821
Biso mean--37.72 29.22 -
Num. residues----988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0128203
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167403
X-RAY DIFFRACTIONr_angle_refined_deg1.7411.6411141
X-RAY DIFFRACTIONr_angle_other_deg0.5891.55417296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.77451023
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.3661042
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.52101293
X-RAY DIFFRACTIONr_chiral_restr0.090.21213
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.029327
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021605
LS refinement shellResolution: 1.504→1.543 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 552 -
Rwork0.242 10767 -
all-11319 -
obs--99.12 %

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