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- PDB-3wgb: Crystal structure of aeromonas jandaei L-allo-threonine aldolase -

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Basic information

Entry
Database: PDB / ID: 3wgb
TitleCrystal structure of aeromonas jandaei L-allo-threonine aldolase
ComponentsL-allo-threonine aldolase
KeywordsLYASE / PYRIDOXAL-5'-PHOSPHATE / threonine aldolase
Function / homology
Function and homology information


L-allo-threonine aldolase / L-allo-threonine aldolase activity / glycine biosynthetic process / 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
GLYCINE / Chem-PLG / L-allo-threonine aldolase
Similarity search - Component
Biological speciesAeromonas jandaei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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

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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)147,7519
Polymers146,4514
Non-polymers1,3005
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13510 Å2
ΔGint-48 kcal/mol
Surface area42410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.474, 95.850, 94.884
Angle α, β, γ (deg.)90.00, 113.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 36612.867 Da / Num. of mol.: 4
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: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 45% MPD, 0.1M HEPES-NAOH (PH7.5), 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: May 13, 2009
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: 2.59→86.92 Å / Num. obs: 41738 / % possible obs: 99.3 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.59→2.63 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.856 / SU B: 12.921 / SU ML: 0.281 / Cross valid method: THROUGHOUT / ESU R Free: 0.379 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2094 5 %RANDOM
Rwork0.233 ---
obs0.235 39376 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20.64 Å2
2--1.09 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9762 0 85 169 10016
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02110030
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0411.9813587
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.651286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00323.242438
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.811151635
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.941588
X-RAY DIFFRACTIONr_chiral_restr0.060.21582
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217536
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2061.56428
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.383210196
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.4533602
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.8084.53384
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 158 -
Rwork0.26 2920 -
obs--99.81 %

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