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- PDB-9e97: L-allo-threonine aldolase from Thermotoga maritima N308E-Y87A-R12... -

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Basic information

Entry
Database: PDB / ID: 9.0E+97
TitleL-allo-threonine aldolase from Thermotoga maritima N308E-Y87A-R122G-P121D Mutant with a 2-(aminomethyl)pyridine PLP modification
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: 1.53 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 7, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,21714
Polymers76,4372
Non-polymers1,78012
Water6,143341
1
A: L-allo-threonine aldolase
B: L-allo-threonine aldolase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)156,43428
Polymers152,8744
Non-polymers3,56024
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area21580 Å2
ΔGint-95 kcal/mol
Surface area44140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.208, 166.022, 93.978
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein L-allo-threonine aldolase


Mass: 38218.570 Da / Num. of mol.: 2
Mutation: Y87A, R122G, P121D, N308E, R340S, K341Q, F342V, S343Q
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

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Non-polymers , 6 types, 353 molecules

#2: Chemical ChemComp-A1BGC / {5-hydroxy-6-methyl-4-[(E)-{[(pyridin-2-yl)methyl]imino}methyl]pyridin-3-yl}methyl dihydrogen phosphate


Mass: 337.268 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H16N3O5P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.4 Å3/Da / Density % sol: 48.83 %
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 / 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: 1.53→29.56 Å / Num. obs: 109793 / % possible obs: 99.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 13.79 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.028 / Rrim(I) all: 0.072 / Χ2: 0.99 / Net I/σ(I): 19.2
Reflection shellResolution: 1.53→1.57 Å / % possible obs: 97.8 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.702 / Num. measured all: 45592 / Num. unique obs: 7905 / CC1/2: 0.769 / Rpim(I) all: 0.317 / Rrim(I) all: 0.772 / Χ2: 0.8 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→29.56 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1856 5211 4.91 %
Rwork0.1694 --
obs0.1702 106220 96.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.53→29.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5250 0 113 341 5704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065579
X-RAY DIFFRACTIONf_angle_d0.8537535
X-RAY DIFFRACTIONf_dihedral_angle_d11.8532153
X-RAY DIFFRACTIONf_chiral_restr0.054854
X-RAY DIFFRACTIONf_plane_restr0.005986
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.550.29581500.27093102X-RAY DIFFRACTION90
1.55-1.570.2781610.24873311X-RAY DIFFRACTION95
1.57-1.590.26451800.23613291X-RAY DIFFRACTION95
1.59-1.610.25281490.22973303X-RAY DIFFRACTION96
1.61-1.630.25241380.22353298X-RAY DIFFRACTION95
1.63-1.650.24171610.21333288X-RAY DIFFRACTION95
1.65-1.680.23471750.21013286X-RAY DIFFRACTION95
1.68-1.70.23741600.21173279X-RAY DIFFRACTION95
1.7-1.730.28131550.19673297X-RAY DIFFRACTION96
1.73-1.760.21481780.18733308X-RAY DIFFRACTION95
1.76-1.790.18972080.19343245X-RAY DIFFRACTION95
1.79-1.820.22941640.18423298X-RAY DIFFRACTION95
1.82-1.850.2311630.18753270X-RAY DIFFRACTION95
1.85-1.890.20761740.18213316X-RAY DIFFRACTION96
1.89-1.930.20631710.17543368X-RAY DIFFRACTION97
1.93-1.980.19391710.17173352X-RAY DIFFRACTION97
1.98-2.030.22161700.1653398X-RAY DIFFRACTION96
2.03-2.080.16491790.16313349X-RAY DIFFRACTION97
2.08-2.140.17361700.15513400X-RAY DIFFRACTION98
2.14-2.210.19961200.15923445X-RAY DIFFRACTION98
2.21-2.290.17031820.16243414X-RAY DIFFRACTION98
2.29-2.380.16822040.15943366X-RAY DIFFRACTION98
2.38-2.490.17451910.16243403X-RAY DIFFRACTION98
2.49-2.620.1892030.15883431X-RAY DIFFRACTION99
2.62-2.790.16521630.15683491X-RAY DIFFRACTION99
2.79-30.16591810.16013466X-RAY DIFFRACTION99
3-3.30.17511840.16023501X-RAY DIFFRACTION100
3.3-3.780.15642130.15743496X-RAY DIFFRACTION100
3.78-4.760.16492200.14513543X-RAY DIFFRACTION100
4.76-29.560.17411730.1693694X-RAY DIFFRACTION99

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