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- PDB-4kwf: Crystal Structure Analysis of ALDH2+ALDiB33 -

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Basic information

Entry
Database: PDB / ID: 4kwf
TitleCrystal Structure Analysis of ALDH2+ALDiB33
ComponentsAldehyde dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE/Inhibitor / ALDH2+ALDiB33 / ketone binding / OXIDOREDUCTASE-Inhibitor complex
Function / homology
Function and homology information


Metabolism of serotonin / nitroglycerin reductase activity / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / aldehyde catabolic process / alcohol metabolic process / phenylacetaldehyde dehydrogenase activity / 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 / aldehyde catabolic process / alcohol metabolic process / phenylacetaldehyde dehydrogenase activity / 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
1-benzyl-1H-indole-2,3-dione / GUANIDINE / Aldehyde dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.31 Å
AuthorsHurley, T.D. / Kimble-Hill, A.C.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Development of selective inhibitors for aldehyde dehydrogenases based on substituted indole-2,3-diones.
Authors: Kimble-Hill, A.C. / Parajuli, B. / Chen, C.H. / Mochly-Rosen, D. / Hurley, T.D.
History
DepositionMay 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software

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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
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)433,80435
Polymers431,7618
Non-polymers2,04327
Water3,387188
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)216,93118
Polymers215,8804
Non-polymers1,05114
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23740 Å2
ΔGint-88 kcal/mol
Surface area59090 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)216,87217
Polymers215,8804
Non-polymers99213
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23350 Å2
ΔGint-98 kcal/mol
Surface area59060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.293, 177.092, 102.551
Angle α, β, γ (deg.)90.000, 94.390, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

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


Mass: 53970.090 Da / Num. of mol.: 8 / Fragment: UNP residues 24-517
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH2, ALDM / 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, 215 molecules

#2: Chemical
ChemComp-3AK / 1-benzyl-1H-indole-2,3-dione


Mass: 237.253 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H11NO2
#3: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GAI / GUANIDINE / Guanidine


Mass: 59.070 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH5N3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.15 Å3/Da / Density % sol: 42.66 %
Crystal growTemperature: 300 K / Method: sitting drop / pH: 6.4
Details: 100 mM ACES, 100 mm guanidine-HCl, 10 mm MgCl2, and 14-19% PEG 6000, pH 6.4, sitting drop, temperature 300K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorDetector: CCD / Date: Nov 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 158074 / % possible obs: 98.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.081 / Χ2: 1.038 / Net I/σ(I): 12.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.342.90.51976911.037197
2.34-2.3830.4977711.037198.4
2.38-2.4330.47578301.039199
2.43-2.483.10.42578380.911199.5
2.48-2.533.10.38578271.063199.5
2.53-2.593.20.31478591.094199.5
2.59-2.663.20.28778501.163199.5
2.66-2.733.20.26978631.171199.6
2.73-2.813.20.20178761.109199.5
2.81-2.93.20.16579081.036199.6
2.9-33.20.13778941.024199.6
3-3.123.20.10978161.022199.5
3.12-3.263.20.09478701.009199.4
3.26-3.443.20.08778831.027199.4
3.44-3.653.20.07978961.038199.5
3.65-3.933.20.07578781.009199.2
3.93-4.333.20.06778410.953199.1
4.33-4.953.10.05478281.014198.7
4.95-6.243.10.04378570.924198.6
6.24-503.10.03275151.078193.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
REFMAC5.7.0029phasing
RefinementResolution: 2.31→49.12 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.895 / Occupancy max: 1 / Occupancy min: 1 / SU B: 9.511 / SU ML: 0.236 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.595 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2961 8008 5.1 %RANDOM
Rwork0.2389 150293 --
obs0.2418 150065 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.11 Å2 / Biso mean: 53.1268 Å2 / Biso min: 24.58 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.31→49.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30384 0 140 188 30712
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01931181
X-RAY DIFFRACTIONr_bond_other_d0.0010.0229551
X-RAY DIFFRACTIONr_angle_refined_deg1.1881.95442301
X-RAY DIFFRACTIONr_angle_other_deg0.738367901
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1253944
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.24624.6291400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.929155040
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.10115160
X-RAY DIFFRACTIONr_chiral_restr0.0640.24632
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02136012
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027259
LS refinement shellResolution: 2.31→2.365 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 561 -
Rwork0.249 10021 -
all-10582 -
obs--89.69 %

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