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- PDB-3iau: The structure of the processed form of threonine deaminase isofor... -

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Basic information

Entry
Database: PDB / ID: 3iau
TitleThe structure of the processed form of threonine deaminase isoform 2 from Solanum lycopersicum
ComponentsThreonine deaminase
KeywordsLYASE / pyridoxal phosphate / Amino-acid biosynthesis / defensive protein / jasmonic acid pathway / jasmonic acid / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS / CESG / Allosteric enzyme / Branched-chain amino acid biosynthesis / Chloroplast / Isoleucine biosynthesis / Transit peptide
Function / homology
Function and homology information


positive regulation of defense response / response to herbivore / threonine ammonia-lyase / defense response to insect / threonine deaminase activity / L-serine ammonia-lyase / response to insect / L-serine ammonia-lyase activity / L-threonine catabolic process / L-serine catabolic process ...positive regulation of defense response / response to herbivore / threonine ammonia-lyase / defense response to insect / threonine deaminase activity / L-serine ammonia-lyase / response to insect / L-serine ammonia-lyase activity / L-threonine catabolic process / L-serine catabolic process / isoleucine biosynthetic process / chloroplast / pyridoxal phosphate binding / protein homotetramerization / identical protein binding
Similarity search - Function
Threonine dehydratase, biosynthetic / Threonine dehydratase, ACT-like domain / Threonine dehydratase, ACT-like domain superfamily / C-terminal regulatory domain of Threonine dehydratase / ACT-like domain profile. / : / Serine/threonine dehydratase, pyridoxal-phosphate-binding site / Serine/threonine dehydratases pyridoxal-phosphate attachment site. / ACT-like domain / Rossmann fold - #1100 ...Threonine dehydratase, biosynthetic / Threonine dehydratase, ACT-like domain / Threonine dehydratase, ACT-like domain superfamily / C-terminal regulatory domain of Threonine dehydratase / ACT-like domain profile. / : / Serine/threonine dehydratase, pyridoxal-phosphate-binding site / Serine/threonine dehydratases pyridoxal-phosphate attachment site. / ACT-like domain / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Threonine dehydratase 2 biosynthetic, chloroplastic
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.353 Å
AuthorsBianchetti, C.M. / Bingman, C.A. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Adaptive evolution of threonine deaminase in plant defense against insect herbivores.
Authors: Gonzales-Vigil, E. / Bianchetti, C.M. / Phillips, G.N. / Howe, G.A.
History
DepositionJul 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Threonine deaminase
B: Threonine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1187
Polymers78,3152
Non-polymers1,8035
Water11,782654
1
A: Threonine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9025
Polymers39,1581
Non-polymers1,7444
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Threonine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2172
Polymers39,1581
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)136.834, 136.834, 254.226
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Threonine deaminase / Threonine dehydratase biosynthetic / chloroplastic / TD


Mass: 39157.629 Da / Num. of mol.: 2 / Fragment: sequence database residues 53-415
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: TD / Plasmid: pET30TD / Production host: Escherichia coli (E. coli) / Strain (production host): Bl24 (DE3) / References: UniProt: P25306, threonine ammonia-lyase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


Mass: 1529.829 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 654 / Source method: isolated from a natural source / Formula: H2O
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: 4.42 Å3/Da / Density % sol: 72.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Protein Solution (10 mg/ml protein, 0.05 M NaCl, 0.003 M NaN3, 0.005 M Bis-Tris pH 7) mixed in a 1:1 ratio with the Well Solution (32% Polyethylene glycol 1500, 0.1 M LiSO4, 0.1 M Sodium ...Details: Protein Solution (10 mg/ml protein, 0.05 M NaCl, 0.003 M NaN3, 0.005 M Bis-Tris pH 7) mixed in a 1:1 ratio with the Well Solution (32% Polyethylene glycol 1500, 0.1 M LiSO4, 0.1 M Sodium Acetate pH 4.5). Cryoprotected with 32% Polyethylene glycol 1500, 0.1 M LiSO4, 5% ethylene glycol, 0.1 M Sodium Acetate pH 4.5, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97957 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 6, 2009 / Details: mirrors and beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionRedundancy: 21.5 % / Av σ(I) over netI: 28.11 / Number: 1263122 / Rmerge(I) obs: 0.133 / Χ2: 1.04 / D res high: 2.35 Å / D res low: 50 Å / Num. obs: 58877 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.065010010.0420.91820.7
4.025.0610010.0680.96421.8
3.514.0210010.0771.01622.1
3.193.5110010.1241.02722.2
2.963.1910010.191.06822.2
2.792.9610010.2441.08922
2.652.7910010.3271.07121.7
2.532.6510010.4241.08621.3
2.432.5310010.5421.08220.7
2.352.4310010.6761.10919.9
ReflectionResolution: 2.35→50 Å / Num. obs: 58877 / % possible obs: 100 % / Redundancy: 21.5 % / Biso Wilson estimate: 26.65 Å2 / Rmerge(I) obs: 0.133 / Χ2: 1.041 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.35-2.4319.90.67657761.109100
2.43-2.5320.70.54257751.082100
2.53-2.6521.30.42457851.086100
2.65-2.7921.70.32757941.071100
2.79-2.96220.24458221.089100
2.96-3.1922.20.1958231.068100
3.19-3.5122.20.12458731.027100
3.51-4.0222.10.07759201.016100
4.02-5.0621.80.06859820.964100
5.06-5020.70.04263270.918100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.376 / Cor.coef. Fo:Fc: 0.662
Highest resolutionLowest resolution
Rotation3 Å48.56 Å
Translation3 Å48.56 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.353→48.559 Å / Occupancy max: 1 / Occupancy min: 0.04 / SU ML: 1.96 / σ(F): 1.34 / Phase error: 17.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.199 2979 5.07 %
Rwork0.164 --
obs0.166 58785 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.526 Å2 / ksol: 0.329 e/Å3
Displacement parametersBiso max: 118.12 Å2 / Biso mean: 32.753 Å2 / Biso min: 9.06 Å2
Baniso -1Baniso -2Baniso -3
1-1.684 Å20 Å2-0 Å2
2--1.684 Å20 Å2
3----3.368 Å2
Refinement stepCycle: LAST / Resolution: 2.353→48.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5324 0 40 654 6018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055484
X-RAY DIFFRACTIONf_angle_d0.9147435
X-RAY DIFFRACTIONf_chiral_restr0.061861
X-RAY DIFFRACTIONf_plane_restr0.003963
X-RAY DIFFRACTIONf_dihedral_angle_d16.4091997
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.353-2.3920.2221280.1992511263996
2.392-2.4330.2311390.18525962735100
2.433-2.4780.2191230.17426282751100
2.478-2.5250.2011640.16826022766100
2.525-2.5770.2271210.17226342755100
2.577-2.6330.2061400.16326412781100
2.633-2.6940.1861470.15725972744100
2.694-2.7610.2231510.16526192770100
2.761-2.8360.1991440.16326102754100
2.836-2.920.1931560.16326322788100
2.92-3.0140.2381360.16926312767100
3.014-3.1210.1931560.17326302786100
3.121-3.2460.2151420.16426532795100
3.246-3.3940.2111130.16826632776100
3.394-3.5730.2021360.16326602796100
3.573-3.7970.1951420.15126892831100
3.797-4.090.1851400.15126772817100
4.09-4.5010.1641360.13427102846100
4.501-5.1520.1551480.13827192867100
5.152-6.4880.2141520.1727672919100
6.488-48.5690.1831650.1729373102100

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