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- PDB-1tdj: THREONINE DEAMINASE (BIOSYNTHETIC) FROM E. COLI -

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Basic information

Entry
Database: PDB / ID: 1tdj
TitleTHREONINE DEAMINASE (BIOSYNTHETIC) FROM E. COLI
ComponentsBIOSYNTHETIC THREONINE DEAMINASE
KeywordsALLOSTERY / COOPERATIVE / TETRAMER / REGULATION / PYRIDOXAL PHOSPHATE / ISOLEUCINE BIOSYNTHESIS
Function / homology
Function and homology information


threonine ammonia-lyase / threonine deaminase activity / threonine catabolic process / threonine metabolic process / branched-chain amino acid biosynthetic process / isoleucine biosynthetic process / amino acid binding / pyridoxal phosphate binding
Similarity search - Function
Biosynthetic Threonine Deaminase; domain 3 / Biosynthetic Threonine Deaminase; Domain 3 / Threonine dehydratase, ACT-like domain / Threonine dehydratase, biosynthetic / 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. / Rossmann fold - #1100 ...Biosynthetic Threonine Deaminase; domain 3 / Biosynthetic Threonine Deaminase; Domain 3 / Threonine dehydratase, ACT-like domain / Threonine dehydratase, biosynthetic / 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. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / L-threonine dehydratase biosynthetic IlvA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.8 Å
AuthorsGallagher, D.T. / Gilliland, G.L. / Xiao, G. / Eisenstein, E.
Citation
Journal: Structure / Year: 1998
Title: Structure and control of pyridoxal phosphate dependent allosteric threonine deaminase.
Authors: Gallagher, D.T. / Gilliland, G.L. / Xiao, G. / Zondlo, J. / Fisher, K.E. / Chinchilla, D. / Eisenstein, E.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Polymorphous Crystallization and Diffraction of Threonine Deaminase from Escherichia Coli
Authors: Gallagher, D.T. / Eisenstein, E. / Fisher, K.E. / Zondlo, J. / Chinchilla, D. / Yu, H.D. / Dill, J. / Winborne, E. / Ducote, K. / Xiao, G. / Gilliland, G.L.
History
DepositionMar 27, 1998Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BIOSYNTHETIC THREONINE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5102
Polymers56,2631
Non-polymers2471
Water59433
1
A: BIOSYNTHETIC THREONINE DEAMINASE
hetero molecules

A: BIOSYNTHETIC THREONINE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,0204
Polymers112,5262
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)85.100, 90.800, 162.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein BIOSYNTHETIC THREONINE DEAMINASE / THREONINE DEHYDRATASE


Mass: 56263.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SCHIFF BASE LINKAGE BETWEEN LYS 62 AND PLP / Source: (natural) Escherichia coli (E. coli) / Cellular location: CYTOPLASM / References: UniProt: P04968, EC: 4.2.1.16
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 46 % / Description: C-DOMAIN IMAGED BY IMR
Crystal growpH: 8
Details: PROTEIN AT 40 MG/ML WAS MIXED WITH, THEN EQUILIBRATED OVER 11% PEG 4K, 40 MM TRIS 8.0, 60 MM MGCL2, AT RT.
Temp details: room temp
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Details: Gallagher, D.T., (1998) Acta Crystallogr.,Sect.D, 54, 467.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 %PEG40001reservoir
240 mMTris1reservoir
370 mM1reservoirMgCl2
40.2 M1reservoirKCl
530 mg/mlprotain1drop
650 mMpotassium phosphate1drop
70.1 mMdithiothreitol1drop
80.1 mMethylene diamine tetraacetic acid1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Sep 1, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→16 Å / Num. obs: 13860 / % possible obs: 78 % / Observed criterion σ(I): 0.5 / Redundancy: 2 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.088 / Net I/σ(I): 14
Reflection shellResolution: 2.7→2.86 Å / Redundancy: 1 % / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.372 / % possible all: 30

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Processing

Software
NameVersionClassification
PHASESphasing
TNT5Erefinement
XENGENdata reduction
XENGENdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.8→16 Å / Isotropic thermal model: TNT BCORREL V1.0 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
Details: THE 61 ATOMS WITH B=100.0 MUST BE CONSIDERED TO BE MARGINALLY ORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.34 1009 7.5 %RANDOM SUBSET
Rwork0.2 ---
all0.21 13542 --
obs0.21 13542 86 %-
Solvent computationSolvent model: BABINET SCALING / Bsol: 150 Å2 / ksol: 0.56 e/Å3
Refinement stepCycle: LAST / Resolution: 2.8→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3800 0 15 33 3848
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0238910.8
X-RAY DIFFRACTIONt_angle_deg2.952381.7
X-RAY DIFFRACTIONt_dihedral_angle_d21.423300
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.018941
X-RAY DIFFRACTIONt_gen_planes0.0225783
X-RAY DIFFRACTIONt_it2.1387522
X-RAY DIFFRACTIONt_nbd0.03213517
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg21.40
X-RAY DIFFRACTIONt_planar_d0.0181
X-RAY DIFFRACTIONt_plane_restr0.0223

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