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- PDB-3wgc: Aeromonas jandaei L-allo-threonine aldolase H128Y/S292R double mutant -

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Basic information

Entry
Database: PDB / ID: 3wgc
TitleAeromonas jandaei L-allo-threonine aldolase H128Y/S292R double mutant
ComponentsL-allo-threonine aldolase
KeywordsLYASE / PYRIDOXAL-5'-PHOSPHATE / threonine aldolase
Function / homology
Function and homology information


L-allo-threonine aldolase / glycine biosynthetic process / L-allo-threonine aldolase activity / threonine catabolic process / cytosol
Similarity search - Function
Low specificity L-threonine aldolase / 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 / 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-PLG / L-allo-threonine aldolase
Similarity search - Component
Biological speciesAeromonas jandaei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsQin, H.M. / Imai, F.L. / Miyakawa, T. / Kataoka, M. / Okai, M. / Ohtsuka, J. / Hou, F. / Nagata, K. / Shimizu, S. / Tanokura, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: L-allo-Threonine aldolase with an H128Y/S292R mutation from Aeromonas jandaei DK-39 reveals the structural basis of changes in substrate stereoselectivity.
Authors: Qin, H.M. / Imai, F.L. / Miyakawa, T. / Kataoka, M. / Kitamura, N. / Urano, N. / Mori, K. / Kawabata, H. / Okai, M. / Ohtsuka, J. / Hou, F. / Nagata, K. / Shimizu, S. / Tanokura, M.
History
DepositionAug 3, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)148,0578
Polymers146,8324
Non-polymers1,2254
Water6,539363
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12880 Å2
ΔGint-46 kcal/mol
Surface area42510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.780, 93.360, 94.020
Angle α, β, γ (deg.)90.00, 113.92, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11CHAIN A
21CHAIN B
31CHAIN C
41CHAIN D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 2 - 336 / Label seq-ID: 5 - 339

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1CHAIN AAA
2CHAIN BBB
3CHAIN CCC
4CHAIN DDD

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Components

#1: Protein
L-allo-threonine aldolase / L-allo-TA / L-allo-threonine acetaldehyde-lyase


Mass: 36708.012 Da / Num. of mol.: 4 / Mutation: H128Y, S292R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas jandaei (bacteria) / Gene: LATA, ltaA / Plasmid: PET-28A / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA (DE3) / References: UniProt: O07051, L-allo-threonine aldolase
#2: Chemical
ChemComp-PLG / N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] / N-PYRIDOXYL-GLYCINE-5-MONOPHOSPHATE


Mass: 306.209 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N2O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.15 Å3/Da / Density % sol: 42.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 34% MPD, 0.1M MES-NAOH (PH6.5), 0.2M AMMONIUM ACETATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 2, 2010
RadiationMonochromator: NUMERICAL LINK TYPE SI(111) DOUBLE CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 42773 / % possible obs: 98.8 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.5→2.56 Å / % possible all: 98.5

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Processing

Software
NameVersionClassification
MOLREPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→46.661 Å / SU ML: 0.3 / σ(F): 1.36 / Phase error: 27.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2473 2152 5.04 %
Rwork0.1863 --
obs0.1894 42715 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→46.661 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9743 0 80 363 10186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039998
X-RAY DIFFRACTIONf_angle_d0.83913577
X-RAY DIFFRACTIONf_dihedral_angle_d13.8633583
X-RAY DIFFRACTIONf_chiral_restr0.0291586
X-RAY DIFFRACTIONf_plane_restr0.0041775
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A5822X-RAY DIFFRACTIONTORSIONAL
12B5822X-RAY DIFFRACTIONTORSIONAL
13C5822X-RAY DIFFRACTIONTORSIONAL
14D5822X-RAY DIFFRACTIONTORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.55810.32921470.21912647X-RAY DIFFRACTION98
2.5581-2.62210.2691420.21032695X-RAY DIFFRACTION100
2.6221-2.6930.29291500.21022697X-RAY DIFFRACTION99
2.693-2.77220.3021380.20662722X-RAY DIFFRACTION99
2.7722-2.86170.31291500.20532683X-RAY DIFFRACTION100
2.8617-2.9640.26891220.20352735X-RAY DIFFRACTION99
2.964-3.08260.28131480.19782688X-RAY DIFFRACTION99
3.0826-3.22290.26151520.20542710X-RAY DIFFRACTION99
3.2229-3.39270.3011320.19452707X-RAY DIFFRACTION99
3.3927-3.60520.26451510.18632683X-RAY DIFFRACTION98
3.6052-3.88350.20121440.16782671X-RAY DIFFRACTION98
3.8835-4.2740.2131390.15912684X-RAY DIFFRACTION98
4.274-4.89190.20321480.16342725X-RAY DIFFRACTION99
4.8919-6.16110.23371580.19522727X-RAY DIFFRACTION100
6.1611-46.66930.20991310.17532789X-RAY DIFFRACTION99

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