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- PDB-3aex: Catalytic intermediate analogue of threonine synthase from Thermu... -

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Basic information

Entry
Database: PDB / ID: 3aex
TitleCatalytic intermediate analogue of threonine synthase from Thermus thermophilus HB8
ComponentsThreonine synthase
KeywordsLYASE / Threonine synthase / PLP / Pyridoxal phosphate
Function / homology
Function and homology information


threonine synthase / threonine synthase activity / threonine biosynthetic process / cysteine biosynthetic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Threonine synthase, bacterial/archaeal / Threonine synthase-like / Serine/threonine dehydratase, pyridoxal-phosphate-binding site / Serine/threonine dehydratases pyridoxal-phosphate attachment site. / Rhodanese domain profile. / Rhodanese-like domain / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme ...Threonine synthase, bacterial/archaeal / Threonine synthase-like / Serine/threonine dehydratase, pyridoxal-phosphate-binding site / Serine/threonine dehydratases pyridoxal-phosphate attachment site. / Rhodanese domain profile. / Rhodanese-like domain / 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
Chem-AN7 / PHOSPHATE ION / Threonine synthase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMurakawa, T. / Machida, Y. / Hayashi, H.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Product-assisted catalysis as the basis of the reaction specificity of threonine synthase.
Authors: Murakawa, T. / Machida, Y. / Hayashi, H.
History
DepositionFeb 13, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Threonine synthase
B: Threonine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9346
Polymers74,1092
Non-polymers8244
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6720 Å2
ΔGint-56 kcal/mol
Surface area23040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.252, 115.252, 99.709
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Threonine synthase


Mass: 37054.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0491 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SL02, threonine synthase
#2: Chemical ChemComp-AN7 / (3E)-4-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}-2-oxobut-3-enoic acid


Mass: 317.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12NO8P
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.58 Å3/Da / Density % sol: 52.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.1M Na/K phosphate, 10%(w/v) PEG 3000, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: May 19, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 92864 / % possible obs: 100 % / Observed criterion σ(I): 11 / Redundancy: 5.7 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 32.47
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.721 / Mean I/σ(I) obs: 3.016 / Num. unique all: 92864 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V7C

1v7c


Resolution: 2.1→37.7 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.253 2238 -RANDOM
Rwork0.216 ---
obs0.216 44318 98.5 %-
Displacement parametersBiso mean: 42.2 Å2
Baniso -1Baniso -2Baniso -3
1-8.35 Å20 Å20 Å2
2--8.35 Å20 Å2
3----16.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.1→37.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5216 0 52 252 5520
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006142
X-RAY DIFFRACTIONc_angle_deg1.43925
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d1
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.018
RfactorNum. reflection% reflection
Rfree0.339 350 -
Rwork0.314 --
obs--95.9 %

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