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- PDB-1kl7: Crystal Structure of Threonine Synthase from Yeast -

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Basic information

Entry
Database: PDB / ID: 1kl7
TitleCrystal Structure of Threonine Synthase from Yeast
ComponentsThreonine Synthase
KeywordsLYASE / threonine synthesis / pyridoxal 5-phosphate / beta-family / monomer
Function / homology
Function and homology information


threonine synthase / threonine synthase activity / threonine biosynthetic process / pyridoxal phosphate binding / nucleus / cytoplasm
Similarity search - Function
threonine synthase, domain 1, chain A / Threonine synthase, N-terminal domain / Threonine synthase, N-terminal / Threonine synthase, N-terminal domain superfamily / Threonine synthase N terminus / Threonine synthase-like / Serine/threonine dehydratase, pyridoxal-phosphate-binding site / Serine/threonine dehydratases pyridoxal-phosphate attachment site. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme ...threonine synthase, domain 1, chain A / Threonine synthase, N-terminal domain / Threonine synthase, N-terminal / Threonine synthase, N-terminal domain superfamily / Threonine synthase N terminus / Threonine synthase-like / 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 / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Threonine synthase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsGarrido-Franco, M. / Ehlert, S. / Messerschmidt, A. / Marinkovic, S. / Huber, R. / Laber, B. / Bourenkov, G.P. / Clausen, T.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Structure and function of threonine synthase from yeast.
Authors: Garrido-Franco, M. / Ehlert, S. / Messerschmidt, A. / Marinkovic, S. / Huber, R. / Laber, B. / Bourenkov, G.P. / Clausen, T.
History
DepositionDec 11, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Threonine Synthase
B: Threonine Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,2294
Polymers115,7342
Non-polymers4942
Water6,017334
1
A: Threonine Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1142
Polymers57,8671
Non-polymers2471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Threonine Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1142
Polymers57,8671
Non-polymers2471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.3, 51.6, 106.9
Angle α, β, γ (deg.)90, 99.6, 90
Int Tables number4
Space group name H-MP1211
DetailsThe monomer is the functional unit of yeast threonine synthase. There are two such monomers in the asymmetric unit of the P21 crystals.

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Components

#1: Protein Threonine Synthase /


Mass: 57867.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P16120, EC: 4.2.99.2
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.24 Å3/Da / Density % sol: 45.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: Hepes/NaOH, PEG4000, Dioxan, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
20.1 MHEPES-NaOH1reservoirpH7.6
320 %PEG40001reservoir
410 %dioxane1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.92, 0.98, 0.9874
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 28, 1999
RadiationMonochromator: Si FILTER / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.921
20.981
30.98741
ReflectionResolution: 2.7→20 Å / Num. all: 28542 / Num. obs: 28407 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.063 / Net I/σ(I): 16.8
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.172 / Mean I/σ(I) obs: 4.6 / % possible all: 97.3
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 54312 / Num. measured all: 145806 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 97.3 % / Rmerge(I) obs: 0.172

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Processing

Software
NameVersionClassification
SHARPphasing
CNS0.9refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.7→20 Å / Isotropic thermal model: isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2526 1381 -RANDOM
Rwork0.2009 ---
all-28386 --
obs-28386 98.8 %-
Displacement parametersBiso mean: 43 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7930 0 30 334 8294
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_mcbond_it0.98
Refinement
*PLUS
Lowest resolution: 8 Å / % reflection Rfree: 4.8 % / Rfactor obs: 0.212 / Rfactor Rfree: 0.252 / Rfactor Rwork: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0082
X-RAY DIFFRACTIONc_angle_deg1.35

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