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- PDB-8pus: Tha1 L-threonine aldolase (mouse), orthorhombic form (F222) -

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Basic information

Entry
Database: PDB / ID: 8pus
TitleTha1 L-threonine aldolase (mouse), orthorhombic form (F222)
ComponentsL-threonine aldolase
KeywordsLYASE / amino acid metabolic process / threonine aldolase / hydroxy trimethyl-lysine aldolase / carnitine biosynthesis / PLP-dependent enzyme
Function / homologyLow specificity L-threonine aldolase / Aromatic amino acid beta-eliminating lyase/threonine aldolase / Beta-eliminating lyase / amino acid metabolic process / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / lyase activity / L-threonine aldolase
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 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

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Assembly

Deposited unit
A: L-threonine aldolase


Theoretical massNumber of molelcules
Total (without water)41,5531
Polymers41,5531
Non-polymers00
Water1,02757
1
A: L-threonine aldolase

A: L-threonine aldolase

A: L-threonine aldolase

A: L-threonine aldolase


Theoretical massNumber of molelcules
Total (without water)166,2134
Polymers166,2134
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area14310 Å2
ΔGint-29 kcal/mol
Surface area48610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.694, 100.524, 171.257
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Space group name HallF22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x,y+1/2,z+1/2
#6: x,-y+1/2,-z+1/2
#7: -x,y+1/2,-z+1/2
#8: -x,-y+1/2,z+1/2
#9: x+1/2,y,z+1/2
#10: x+1/2,-y,-z+1/2
#11: -x+1/2,y,-z+1/2
#12: -x+1/2,-y,z+1/2
#13: x+1/2,y+1/2,z
#14: x+1/2,-y+1/2,-z
#15: -x+1/2,y+1/2,-z
#16: -x+1/2,-y+1/2,z

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Components

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


Mass: 41553.277 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.17 Å3/Da / Density % sol: 43.24 %
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: 0.873128 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: 0.873128 Å / Relative weight: 1
ReflectionResolution: 2.26→25.71 Å / Num. obs: 17051 / % possible obs: 99.7 % / Redundancy: 9.9 % / Biso Wilson estimate: 46.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.027 / Rrim(I) all: 0.088 / Net I/σ(I): 16.6
Reflection shellResolution: 2.26→2.33 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1561 / CC1/2: 0.881 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→25.71 Å / SU ML: 0.3255 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 29.9735
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.24 880 5.17 %
Rwork0.2097 16148 -
obs0.2113 17028 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.74 Å2
Refinement stepCycle: LAST / Resolution: 2.26→25.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2753 0 0 57 2810
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00322865
X-RAY DIFFRACTIONf_angle_d0.59613899
X-RAY DIFFRACTIONf_chiral_restr0.042441
X-RAY DIFFRACTIONf_plane_restr0.017519
X-RAY DIFFRACTIONf_dihedral_angle_d12.29121057
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.40.3181520.32172641X-RAY DIFFRACTION99.29
2.4-2.590.32021340.28442666X-RAY DIFFRACTION99.75
2.59-2.850.3151490.26252673X-RAY DIFFRACTION99.65
2.85-3.260.24691490.23412698X-RAY DIFFRACTION99.79
3.26-4.10.22671470.19872690X-RAY DIFFRACTION99.44
4.1-25.710.20671490.17132780X-RAY DIFFRACTION98.95
Refinement TLS params.Method: refined / Origin x: 17.9600826505 Å / Origin y: -3.11695741741 Å / Origin z: -20.4440244358 Å
111213212223313233
T0.35425706462 Å20.0200577655813 Å20.0517388709173 Å2-0.559364156929 Å2-0.0943614464676 Å2--0.397353671738 Å2
L2.67716739866 °20.430650138436 °2-0.11462292348 °2-1.80249268043 °2-0.240286467176 °2--2.2950681657 °2
S-0.0983227332771 Å °0.515145653207 Å °-0.185658749758 Å °-0.170160270847 Å °0.0831819392574 Å °-0.391044448626 Å °-0.0105427066113 Å °0.45862563896 Å °0.0357679103802 Å °
Refinement TLS groupSelection details: all

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