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- PDB-7qk7: Crystal structure of the APO form of ALDH1A3 -

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Basic information

Entry
Database: PDB / ID: 7qk7
TitleCrystal structure of the APO form of ALDH1A3
ComponentsAldehyde dehydrogenase family 1 member A3
KeywordsOXIDOREDUCTASE / ALDH1A3 / Aldehyde dehydrogenase family 1 member A3 / APO
Function / homology
Function and homology information


nucleus accumbens development / optic cup morphogenesis involved in camera-type eye development / olfactory pit development / Harderian gland development / retinal dehydrogenase / embryonic eye morphogenesis / embryonic camera-type eye development / aldehyde dehydrogenase [NAD(P)+] activity / righting reflex / RA biosynthesis pathway ...nucleus accumbens development / optic cup morphogenesis involved in camera-type eye development / olfactory pit development / Harderian gland development / retinal dehydrogenase / embryonic eye morphogenesis / embryonic camera-type eye development / aldehyde dehydrogenase [NAD(P)+] activity / righting reflex / RA biosynthesis pathway / retinal metabolic process / retinoic acid biosynthetic process / aldehyde dehydrogenase (NAD+) activity / retinoic acid metabolic process / retinal dehydrogenase activity / inner ear morphogenesis / thyroid hormone binding / face development / neuromuscular process controlling balance / NAD+ binding / retinol metabolic process / locomotory behavior / protein homotetramerization / positive regulation of apoptotic process / apoptotic process / protein homodimerization activity / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase family / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Aldehyde dehydrogenase family 1 member A3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.289 Å
AuthorsCastellvi, A. / Farres, J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and Universities Spain
CitationJournal: Commun Biol / Year: 2022
Title: Structural and biochemical evidence that ATP inhibits the cancer biomarker human aldehyde dehydrogenase 1A3.
Authors: Castellvi, A. / Pequerul, R. / Barracco, V. / Juanhuix, J. / Pares, X. / Farres, J.
History
DepositionDec 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aldehyde dehydrogenase family 1 member A3
B: Aldehyde dehydrogenase family 1 member A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,19410
Polymers116,3732
Non-polymers8218
Water6,431357
1
A: Aldehyde dehydrogenase family 1 member A3
B: Aldehyde dehydrogenase family 1 member A3
hetero molecules

A: Aldehyde dehydrogenase family 1 member A3
B: Aldehyde dehydrogenase family 1 member A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,38820
Polymers232,7464
Non-polymers1,64216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area22900 Å2
ΔGint-38 kcal/mol
Surface area60050 Å2
Unit cell
Length a, b, c (Å)82.960, 90.133, 159.193
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Aldehyde dehydrogenase family 1 member A3 / Aldehyde dehydrogenase 6 / Retinaldehyde dehydrogenase 3 / RalDH3


Mass: 58186.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH1A3, ALDH6 / Production host: Escherichia coli (E. coli)
References: UniProt: P47895, aldehyde dehydrogenase [NAD(P)+]
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.76 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: The crystallization solution consisted of 100 mM BIS-Tris, pH 5.5, 2-2.2 M ammonium sulfate and 5% PEG 400.

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.289→48.44 Å / Num. obs: 53899 / % possible obs: 98.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 50.09 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.052 / Rrim(I) all: 0.134 / Net I/σ(I): 11
Reflection shellResolution: 2.29→2.35 Å / Rmerge(I) obs: 1.391 / Num. unique obs: 4253 / CC1/2: 0.734

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (18-SEP-2020)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5fhz
Resolution: 2.289→48.44 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.914 / SU R Cruickshank DPI: 0.256 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.263 / SU Rfree Blow DPI: 0.198 / SU Rfree Cruickshank DPI: 0.198
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2559 4.75 %RANDOM
Rwork0.1903 ---
obs0.1921 53879 98.7 %-
Displacement parametersBiso mean: 56.55 Å2
Baniso -1Baniso -2Baniso -3
1--26.4426 Å20 Å20 Å2
2--7.693 Å20 Å2
3---18.7496 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2.289→48.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7359 0 54 357 7770
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0087605HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9810313HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2582SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1286HARMONIC5
X-RAY DIFFRACTIONt_it7605HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.17
X-RAY DIFFRACTIONt_other_torsion17.39
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1016SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6129SEMIHARMONIC4
LS refinement shellResolution: 2.29→2.31 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3538 -3.99 %
Rwork0.2403 1035 -
all0.2442 1078 -
obs--90.5 %

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