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- PDB-9r3z: Exploiting ALDH1A2 and ALDH1A3 Isoform Variability for Crystalliz... -

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Basic information

Entry
Database: PDB / ID: 9r3z
TitleExploiting ALDH1A2 and ALDH1A3 Isoform Variability for Crystallization Screening
ComponentsRetinal dehydrogenase 2
KeywordsOXIDOREDUCTASE / Aldehyde Dehydrogenase / Cancer Stem Cells / Retinaldehyde / ALDH1A3 / structure-based drug discovery
Function / homology
Function and homology information


determination of bilateral symmetry / regulation of vascular endothelial cell proliferation / 3-chloroallyl aldehyde dehydrogenase activity / 9-cis-retinoic acid biosynthetic process / retinoic acid biosynthetic process / retinal dehydrogenase / ureter maturation / embryonic camera-type eye development / midgut development / morphogenesis of embryonic epithelium ...determination of bilateral symmetry / regulation of vascular endothelial cell proliferation / 3-chloroallyl aldehyde dehydrogenase activity / 9-cis-retinoic acid biosynthetic process / retinoic acid biosynthetic process / retinal dehydrogenase / ureter maturation / embryonic camera-type eye development / midgut development / morphogenesis of embryonic epithelium / pituitary gland development / RA biosynthesis pathway / proximal/distal pattern formation / vitamin A metabolic process / neural crest cell development / hindbrain development / retinal metabolic process / embryonic digestive tract development / aldehyde dehydrogenase (NAD+) activity / retinal binding / pancreas development / retinal dehydrogenase (NAD+) activity / embryonic forelimb morphogenesis / response to vitamin A / retinoic acid metabolic process / cardiac muscle tissue development / retinol metabolic process / anterior/posterior pattern specification / neural tube development / blood vessel development / face development / response to retinoic acid / heart morphogenesis / retinoic acid receptor signaling pathway / cellular response to retinoic acid / response to cytokine / lung development / kidney development / liver development / neuron differentiation / response to estradiol / protein homotetramerization / cell population proliferation / positive regulation of apoptotic process / negative regulation of cell population proliferation / positive regulation of cell population proliferation / positive regulation of gene expression / perinuclear region of cytoplasm / cytosol / cytoplasm
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, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
Retinal dehydrogenase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGaraavglia, S. / Mazzorana, M.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of HealthPNRRM6C2-- 12376588 Italy
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2025
Title: Exploiting ALDH1A2 and ALDH1A3 isoform variability for crystallisation screening.
Authors: Siragusa, S. / Garavaglia, S. / Mazzorana, M.
History
DepositionMay 6, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Retinal dehydrogenase 2
B: Retinal dehydrogenase 2
C: Retinal dehydrogenase 2
D: Retinal dehydrogenase 2


Theoretical massNumber of molelcules
Total (without water)227,1354
Polymers227,1354
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16200 Å2
ΔGint-60 kcal/mol
Surface area66700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.841, 139.478, 85.171
Angle α, β, γ (deg.)90.000, 93.927, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Retinal dehydrogenase 2 / RALDH 2 / RalDH2 / Aldehyde dehydrogenase family 1 member A2 / ALDH1A2 / Retinaldehyde-specific ...RALDH 2 / RalDH2 / Aldehyde dehydrogenase family 1 member A2 / ALDH1A2 / Retinaldehyde-specific dehydrogenase type 2 / RALDH(II)


Mass: 56783.688 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH1A2, RALDH2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O94788, retinal dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.16 Å3/Da / Density % sol: 43.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.09 M NPS, 0.1 M Buffer System 3 (1.0M ph 8.5 Tris (base); BICINE 8.5) 30 % v/v Precipitant Mix 3 (40% v/v Glycerol; 20% w/v PEG 4000)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.79→73 Å / Num. obs: 48094 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 62.37 Å2 / CC1/2: 1 / Net I/σ(I): 5.4
Reflection shellResolution: 2.79→2.85 Å / Num. unique obs: 2340 / CC1/2: 0.3

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→72.57 Å / SU ML: 0.4646 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.3178
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2852 2224 4.68 %
Rwork0.2084 45286 -
obs0.212 47510 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.35 Å2
Refinement stepCycle: LAST / Resolution: 2.8→72.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14657 0 0 53 14710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914965
X-RAY DIFFRACTIONf_angle_d1.036220266
X-RAY DIFFRACTIONf_chiral_restr0.05412236
X-RAY DIFFRACTIONf_plane_restr0.00852657
X-RAY DIFFRACTIONf_dihedral_angle_d18.3135516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.860.37191310.32122856X-RAY DIFFRACTION99.6
2.86-2.930.36581440.29672782X-RAY DIFFRACTION99.9
2.93-30.33231120.28442833X-RAY DIFFRACTION99.9
3-3.080.33191200.25922855X-RAY DIFFRACTION100
3.08-3.170.30871360.25252842X-RAY DIFFRACTION99.93
3.17-3.270.36331180.25452832X-RAY DIFFRACTION100
3.27-3.390.33731460.24912810X-RAY DIFFRACTION100
3.39-3.530.29711390.22482802X-RAY DIFFRACTION99.97
3.53-3.690.29741540.21892822X-RAY DIFFRACTION99.97
3.69-3.880.31322000.20532764X-RAY DIFFRACTION100
3.88-4.130.30151370.20122838X-RAY DIFFRACTION99.9
4.13-4.440.3005800.18032868X-RAY DIFFRACTION99.97
4.44-4.890.20961340.15252855X-RAY DIFFRACTION99.97
4.89-5.60.29721700.18882822X-RAY DIFFRACTION100
5.6-7.050.27191580.20322824X-RAY DIFFRACTION99.97
7.05-72.570.21171450.17912881X-RAY DIFFRACTION99.61
Refinement TLS params.Method: refined / Origin x: 20.3729034212 Å / Origin y: -0.19057327886 Å / Origin z: 22.9567880207 Å
111213212223313233
T0.164692312653 Å20.0128668713915 Å2-0.00611903278242 Å2-0.146153159727 Å2-0.029894701961 Å2--0.210276251247 Å2
L0.224895393159 °20.0220649270857 °2-0.012637657571 °2-0.211128701569 °20.0318408631864 °2--0.525085240623 °2
S0.018060183537 Å °-0.00766724126888 Å °-0.00368087462941 Å °-0.0178170704286 Å °-0.0687371223887 Å °0.0624812544463 Å °-0.0147704989335 Å °-0.0168793787878 Å °-2.97636431006E-6 Å °
Refinement TLS groupSelection details: all

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