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- PDB-5vye: Crystal Structure of L-Threonine Aldolase from Pseudomonas putida -

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Basic information

Entry
Database: PDB / ID: 5vye
TitleCrystal Structure of L-Threonine Aldolase from Pseudomonas putida
ComponentsL-threonine aldolase
KeywordsLYASE / PLP / threonine aldolase / L-threonine aldolase / aldolase
Function / homology
Function and homology information


threonine aldolase activity / low-specificity L-threonine aldolase / L-threonine catabolic process
Similarity search - Function
Low specificity L-threonine aldolase, bacteria / Aromatic amino acid beta-eliminating lyase/threonine aldolase / Beta-eliminating lyase / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase ...Low specificity L-threonine aldolase, bacteria / Aromatic amino acid beta-eliminating lyase/threonine aldolase / Beta-eliminating lyase / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PLR / L-threonine aldolase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.275 Å
AuthorsBeaudoin, S.F. / Burg, M.J. / Stewart, J.D.
CitationJournal: To Be Published
Title: Crystal Structure of L-Threonine Aldolase from Pseudomonas putida
Authors: Beaudoin, S.F. / Burg, M.J. / Stewart, J.D.
History
DepositionMay 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: L-threonine aldolase
D: L-threonine aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,11712
Polymers152,8164
Non-polymers1,3018
Water8,629479
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19030 Å2
ΔGint-50 kcal/mol
Surface area44480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)198.167, 186.960, 53.269
Angle α, β, γ (deg.)90.00, 98.92, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
L-threonine aldolase


Mass: 38204.066 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: A3L25_23170, B7H18_06210 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A166JNM8, low-specificity L-threonine aldolase
#2: Chemical
ChemComp-PLR / (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE / 4'-DEOXYPYRIDOXINE PHOSPHATE


Mass: 233.158 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H12NO5P
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / 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: 3.18 Å3/Da / Density % sol: 61.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 2.1 M sodium formate, 0.1 M sodium acetate trihydrate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.275→26.755 Å / Num. obs: 172206 / % possible obs: 99.42 % / Observed criterion σ(I): 2.65 / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.08797 / Rpim(I) all: 0.03654 / Net I/σ(I): 14.5
Reflection shellResolution: 2.275→2.356 Å / Num. unique obs: 87029 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
Coot0.6.1model building
XDSdata reduction
PHENIX(1.11.1_2575: ???)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4lnj

4lnj


Resolution: 2.275→26.754 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2193 3958 2.3 %
Rwork0.1799 --
obs0.1808 172206 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.275→26.754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10612 0 84 479 11175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01511001
X-RAY DIFFRACTIONf_angle_d1.26814914
X-RAY DIFFRACTIONf_dihedral_angle_d13.1656452
X-RAY DIFFRACTIONf_chiral_restr0.1641589
X-RAY DIFFRACTIONf_plane_restr0.0081958
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2747-2.30240.37341200.30835008X-RAY DIFFRACTION81
2.3024-2.33150.311400.26876013X-RAY DIFFRACTION100
2.3315-2.36220.28271420.25546013X-RAY DIFFRACTION100
2.3622-2.39450.31331400.24096072X-RAY DIFFRACTION100
2.3945-2.42870.32231450.23396085X-RAY DIFFRACTION100
2.4287-2.46490.25481390.22625987X-RAY DIFFRACTION100
2.4649-2.50340.30471400.22376030X-RAY DIFFRACTION100
2.5034-2.54440.2681450.21346098X-RAY DIFFRACTION100
2.5444-2.58830.2511410.20575957X-RAY DIFFRACTION100
2.5883-2.63530.24571420.20246065X-RAY DIFFRACTION100
2.6353-2.68590.2441430.19676077X-RAY DIFFRACTION100
2.6859-2.74070.20851410.18895992X-RAY DIFFRACTION100
2.7407-2.80020.25871480.20596189X-RAY DIFFRACTION100
2.8002-2.86530.24611390.20465994X-RAY DIFFRACTION100
2.8653-2.93690.27051440.20866033X-RAY DIFFRACTION100
2.9369-3.01620.25831420.2046028X-RAY DIFFRACTION100
3.0162-3.10480.29961420.20036085X-RAY DIFFRACTION100
3.1048-3.20490.2481410.19996027X-RAY DIFFRACTION100
3.2049-3.31920.27091470.19546118X-RAY DIFFRACTION100
3.3192-3.45180.22211400.18885978X-RAY DIFFRACTION100
3.4518-3.60860.2161460.16876084X-RAY DIFFRACTION100
3.6086-3.79830.21841440.15556137X-RAY DIFFRACTION100
3.7983-4.03560.16391370.14815951X-RAY DIFFRACTION100
4.0356-4.34590.14851430.13966048X-RAY DIFFRACTION100
4.3459-4.78110.16821430.13536048X-RAY DIFFRACTION100
4.7811-5.46770.19071400.14876039X-RAY DIFFRACTION100
5.4677-6.86940.21471400.18996054X-RAY DIFFRACTION100
6.8694-26.75590.17751440.16786038X-RAY DIFFRACTION99

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