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- PDB-1e5x: Structure of threonine synthase from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 1e5x
TitleStructure of threonine synthase from Arabidopsis thaliana
ComponentsTHREONINE SYNTHASE
KeywordsTHREONINE BIOSYNTHESIS / PLP ENZYME / S-ADENOSYL-METHIONINE / ALLOSTERY
Function / homology
Function and homology information


threonine synthase / threonine synthase activity / threonine biosynthetic process / cysteine biosynthetic process / chloroplast stroma / chloroplast / pyridoxal phosphate binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Threonine synthase 1, chloroplastic / Threonine synthase 1, chloroplastic
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsThomazeau, K. / Curien, G. / Dumas, R. / Biou, V.
CitationJournal: Protein Sci. / Year: 2001
Title: Crystal Structure of Threonine Synthase from Arabidopsis Thaliana
Authors: Thomazeau, K. / Curien, G. / Dumas, R. / Biou, V.
History
DepositionAug 4, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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


Theoretical massNumber of molelcules
Total (without water)108,1162
Polymers108,1162
Non-polymers00
Water6,990388
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)57.760, 62.140, 76.590
Angle α, β, γ (deg.)109.48, 97.61, 112.74
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.94315, -0.12962, 0.30604), (-0.12904, -0.99139, -0.02223), (0.30628, -0.01853, -0.95176)
Vector: -6.20155, 2.77128, 40.84748)

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Components

#1: Protein THREONINE SYNTHASE


Mass: 54058.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Description: MATURE ENZYME IS WITHOUT TRANSIT PEPTIDE / Cellular location: CHLOROPLAST / Gene: NUCLEAR / Organelle: CHLOROPLAST / Plasmid: PET23 THRC_ARATH / Gene (production host): THRC_ARATH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q39144, UniProt: Q9S7B5*PLUS, EC: 4.2.99.2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUE NUMBERING IN THE PDB FILE CORRESPONDS TO THE MATURE PROTEIN, THEREFORE THERE IS A 40 ...THE RESIDUE NUMBERING IN THE PDB FILE CORRESPONDS TO THE MATURE PROTEIN, THEREFORE THERE IS A 40 AMINOACID DIFFERENCE WITH RESPECT TO THE DATA BASE SEQUENCE.

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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: 1.97 Å3/Da / Density % sol: 38 %
Crystal growpH: 6.5 / Details: 13 % PEG 6000, 1M LICL, MES PH 6.5
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 M1reservoirLiCl
213 %PEG60001reservoir
35 mMdithiothreitol1reservoir
55 mg/mlprotein1drop
4MES-KOH1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978873
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 15, 1999 / Details: MIRRORS
RadiationMonochromator: SI (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978873 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 124846 / % possible obs: 97.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 41.5 Å2 / Rsym value: 0.033 / Net I/σ(I): 8.9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 3 / Rsym value: 0.183 / % possible all: 95.3
Reflection
*PLUS
Highest resolution: 2.25 Å / Num. obs: 43719 / Redundancy: 2.9 % / Num. measured all: 124846 / Rmerge(I) obs: 0.033
Reflection shell
*PLUS
% possible obs: 95.3 % / Redundancy: 2.9 % / Num. unique obs: 6265 / Num. measured obs: 17896 / Rmerge(I) obs: 0.183

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Processing

Software
NameVersionClassification
CNS0.9refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.25→29.81 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1255563.21 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE C-TERMINAL RESIDUE OF MONOMER B WAS NOT SEEN IN THE DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2036 5 %RANDOM
Rwork0.222 ---
obs0.222 41066 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43 Å2 / ksol: 0.334225 e/Å3
Displacement parametersBiso mean: 46.9 Å2
Baniso -1Baniso -2Baniso -3
1-6.13 Å215.46 Å21.26 Å2
2--6.85 Å2-0.94 Å2
3----12.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.25→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6861 0 0 388 7249
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.991.5
X-RAY DIFFRACTIONc_mcangle_it1.732
X-RAY DIFFRACTIONc_scbond_it1.972
X-RAY DIFFRACTIONc_scangle_it2.672.5
Refine LS restraints NCSRms dev Biso : 46 Å2 / Rms dev position: 0.204 Å / Weight Biso : 1 / Weight position: 50
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.356 326 4.8 %
Rwork0.318 6521 -
obs--97.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3SME.PARSME.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87

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