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- PDB-1uin: Crystal Structure of Threonine Synthase from Thermus Thermophilus... -

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Basic information

Entry
Database: PDB / ID: 1uin
TitleCrystal Structure of Threonine Synthase from Thermus Thermophilus HB8, Trigonal Crystal Form
ComponentsThreonine Synthase
KeywordsLYASE / PLP-dependent enzyme / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


threonine synthase / threonine synthase activity / threonine deaminase activity / L-serine ammonia-lyase activity / L-threonine catabolic process / L-serine catabolic process / threonine biosynthetic process / isoleucine biosynthetic process / pyridoxal phosphate binding
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 / 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 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Threonine synthase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.25 Å
AuthorsOmi, R. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.BIOL.CHEM. / Year: 2003
Title: Crystal Structures of Threonine Synthase from Thermus thermophilus HB8: Conformational change, substrate recognition, and mechanism.
Authors: Omi, R. / Masaru, G. / Miyahara, I. / Mizuguchi, H. / Hayashi, H. / Kagamiyama, H. / Hirotsu, K.
History
DepositionJul 17, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 Synthase
B: Threonine Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8927
Polymers74,1092
Non-polymers7825
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-93 kcal/mol
Surface area24030 Å2
MethodPISA
2
A: Threonine Synthase
hetero molecules

A: Threonine Synthase
hetero molecules

B: Threonine Synthase
hetero molecules

B: Threonine Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,78414
Polymers148,2194
Non-polymers1,56510
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation2_654-y+1,x-y,z-1/31
crystal symmetry operation5_565x-y,-y+1,-z+1/31
Buried area10990 Å2
ΔGint-120 kcal/mol
Surface area53130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.207, 113.207, 150.346
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) / Gene: HB8 / Plasmid: pET20b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P83823, threonine synthase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


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


Mass: 18.015 Da / Num. of mol.: 211 / 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: 3.71 Å3/Da / Density % sol: 66.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Ammonium Sulfate, Mes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 MMES1reservoirpH6.5
21.45 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 28, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→20 Å / Num. all: 53148 / Num. obs: 53148 / % possible obs: 99.7 %
Reflection shellResolution: 2.25→2.33 Å / % possible all: 99.4
Reflection
*PLUS
Num. measured all: 486914 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 99.4 % / Rmerge(I) obs: 0.323

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Processing

Software
NameClassification
MOSFLMdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MIR / Resolution: 2.25→10 Å / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.219 5260 RANDOM
Rwork0.191 --
all-52711 -
obs-51814 -
Refine analyzeLuzzati coordinate error obs: 0.24 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.16 Å
Refinement stepCycle: LAST / Resolution: 2.25→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5092 0 45 211 5348
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.92
Refinement
*PLUS
Rfactor Rwork: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92
LS refinement shell
*PLUS
Rfactor Rfree: 0.226 / Rfactor Rwork: 0.211

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