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- PDB-8pum: Tha1 L-threonine aldolase (mouse), monoclinic form (C2) -

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Basic information

Entry
Database: PDB / ID: 8pum
TitleTha1 L-threonine aldolase (mouse), monoclinic form (C2)
ComponentsL-threonine aldolase
KeywordsLYASE / amino acid metabolic process / threonine aldolase / hydroxy trimethyl-lysine aldolase / carnitine biosynthesis / PLP-dependent enzyme
Function / homology
Function and homology information


glycine biosynthetic process / L-allo-threonine aldolase activity / L-threonine catabolic process / cytosol
Similarity search - Function
Low specificity L-threonine aldolase / Aromatic amino acid beta-eliminating lyase/threonine aldolase / Beta-eliminating lyase / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
L-threonine aldolase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBattistutta, R. / Fornasier, E. / Giachin, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: One substrate many enzymes virtual screening uncovers missing genes of carnitine biosynthesis in human and mouse.
Authors: Malatesta, M. / Fornasier, E. / Di Salvo, M.L. / Tramonti, A. / Zangelmi, E. / Peracchi, A. / Secchi, A. / Polverini, E. / Giachin, G. / Battistutta, R. / Contestabile, R. / Percudani, R.
History
DepositionJul 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-threonine aldolase
B: L-threonine aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6094
Polymers83,5632
Non-polymers462
Water52229
1
A: L-threonine aldolase
B: L-threonine aldolase
hetero molecules

A: L-threonine aldolase
B: L-threonine aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,2188
Polymers167,1264
Non-polymers924
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area15160 Å2
ΔGint-74 kcal/mol
Surface area47790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.975, 101.639, 95.958
Angle α, β, γ (deg.)90.00, 116.14, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein L-threonine aldolase / Threonine aldolase 1


Mass: 41781.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tha1, Gly1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6XPS7
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
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: 2.2 Å3/Da / Density % sol: 44.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M sodium nitrate, 0.1 M Bis-Tris propane pH 8.5, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.6→43.07 Å / Num. obs: 21160 / % possible obs: 94.8 % / Redundancy: 5.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.104 / Rrim(I) all: 0.115 / Net I/σ(I): 8.9
Reflection shellResolution: 2.6→2.72 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2662 / CC1/2: 0.786 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→43.07 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2586 1075 5.09 %
Rwork0.2335 --
obs0.2348 21115 94.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→43.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5536 0 2 29 5567
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025648
X-RAY DIFFRACTIONf_angle_d0.567682
X-RAY DIFFRACTIONf_dihedral_angle_d14.5542080
X-RAY DIFFRACTIONf_chiral_restr0.042866
X-RAY DIFFRACTIONf_plane_restr0.0051016
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.720.38731570.40752534X-RAY DIFFRACTION97
2.72-2.860.35861420.342578X-RAY DIFFRACTION98
2.86-3.040.33341640.31492528X-RAY DIFFRACTION97
3.04-3.280.35741250.30782550X-RAY DIFFRACTION96
3.28-3.610.31491290.26562523X-RAY DIFFRACTION96
3.61-4.130.25961250.23132449X-RAY DIFFRACTION92
4.13-5.20.20151170.19672413X-RAY DIFFRACTION91
5.2-43.070.19541160.17252465X-RAY DIFFRACTION90
Refinement TLS params.Method: refined / Origin x: 20.9879 Å / Origin y: -0.2039 Å / Origin z: 22.3706 Å
111213212223313233
T0.6534 Å20.0614 Å2-0.0088 Å2-0.7519 Å20.0466 Å2--0.5525 Å2
L2.7295 °20.3223 °20.0041 °2-0.9607 °20.0336 °2--0.9668 °2
S-0.0044 Å °0.5355 Å °0.0893 Å °-0.1351 Å °0.0051 Å °-0.015 Å °0.0398 Å °0.0151 Å °-0.0215 Å °
Refinement TLS groupSelection details: all

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