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- PDB-9e9j: L-allo-threonine aldolase from Thermotoga maritima, N308E-Y87A-R1... -

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Basic information

Entry
Database: PDB / ID: 9e9j
TitleL-allo-threonine aldolase from Thermotoga maritima, N308E-Y87A-R122G-P121D Mutant
ComponentsL-allo-threonine aldolase
KeywordsLYASE / PYRIDOXAL-5-PHOSPHATE / PLP / ENZYME / INHIBITOR COMPLEX
Function / homology
Function and homology information


glycine biosynthetic process / L-allo-threonine aldolase activity / L-threonine catabolic process / metal ion binding / 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
DI(HYDROXYETHYL)ETHER / L-allo-threonine aldolase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsWang, S. / Jeffrey, P.D. / Sorigue, D. / Hyster, T.K.
Funding supportEuropean Union, United States, 2items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission101063280European Union
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R12GM146043 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Nucleophilic alpha-Functionalization of Benzyl Amines Using an Engineered Threonine Aldolase.
Authors: Ouyang, Y. / Wang, S. / Sorigue, D. / Hyster, T.K.
History
DepositionNov 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-allo-threonine aldolase
B: L-allo-threonine aldolase
C: L-allo-threonine aldolase
D: L-allo-threonine aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,0539
Polymers153,7874
Non-polymers2665
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14620 Å2
ΔGint-108 kcal/mol
Surface area44230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.002, 130.364, 164.195
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
L-allo-threonine aldolase


Mass: 38446.688 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_1744 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X266
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 42.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: HEPES buffer (pH 7.2), Calcium Acetate, PEG 400

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: CONSTANT / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92015 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92015 Å / Relative weight: 1
ReflectionResolution: 2.15→29.33 Å / Num. obs: 72095 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.072 / Rrim(I) all: 0.188 / Net I/σ(I): 9.9
Reflection shellResolution: 2.15→2.2 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.007 / Num. unique obs: 4407 / CC1/2: 0.845 / Rpim(I) all: 0.402 / Rrim(I) all: 1.085 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→29.33 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2515 3642 5.17 %
Rwork0.2035 --
obs0.2061 70378 97.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→29.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10530 0 11 299 10840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710837
X-RAY DIFFRACTIONf_angle_d0.88514671
X-RAY DIFFRACTIONf_dihedral_angle_d13.9384085
X-RAY DIFFRACTIONf_chiral_restr0.0511675
X-RAY DIFFRACTIONf_plane_restr0.0051922
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.180.33341550.26642580X-RAY DIFFRACTION98
2.18-2.210.31411450.25132508X-RAY DIFFRACTION98
2.21-2.240.34781410.2482540X-RAY DIFFRACTION99
2.24-2.270.31561140.24522583X-RAY DIFFRACTION98
2.27-2.310.28711300.22872530X-RAY DIFFRACTION98
2.31-2.350.28311520.23472596X-RAY DIFFRACTION98
2.35-2.390.29431240.24092535X-RAY DIFFRACTION99
2.39-2.430.28831450.22762569X-RAY DIFFRACTION99
2.43-2.480.32361340.24162570X-RAY DIFFRACTION99
2.48-2.530.31761620.22342547X-RAY DIFFRACTION98
2.53-2.580.33471240.24792548X-RAY DIFFRACTION98
2.58-2.640.31191360.24392522X-RAY DIFFRACTION96
2.64-2.710.34241490.24772497X-RAY DIFFRACTION96
2.71-2.780.28831300.2532514X-RAY DIFFRACTION95
2.78-2.860.30791440.2272502X-RAY DIFFRACTION97
2.86-2.960.2731390.21382577X-RAY DIFFRACTION98
2.96-3.060.25511320.21822562X-RAY DIFFRACTION97
3.06-3.180.28411220.22762566X-RAY DIFFRACTION97
3.18-3.330.25961360.21362543X-RAY DIFFRACTION97
3.33-3.50.26891360.20462567X-RAY DIFFRACTION97
3.5-3.720.2191610.19422492X-RAY DIFFRACTION96
3.72-4.010.23391450.17382572X-RAY DIFFRACTION97
4.01-4.410.2021270.15812618X-RAY DIFFRACTION98
4.41-5.050.18411410.15532636X-RAY DIFFRACTION98
5.05-6.350.20561520.17862664X-RAY DIFFRACTION99
6.35-29.330.17491660.16592798X-RAY DIFFRACTION98

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