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- PDB-1v7c: Crystal structure of threonine synthase from thermus thermophilus... -

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Basic information

Entry
Database: PDB / ID: 1v7c
TitleCrystal structure of threonine synthase from thermus thermophilus hb8 in complex with a substrate analogue
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 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-HEY / Threonine synthase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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. / Goto, M. / Miyahara, I. / Mizuguchi, H. / Hayashi, H. / Kagamiyama, H. / Hirotsu, K.
History
DepositionDec 16, 2003Deposition site: PDBJ / Processing site: PDBJ
SupersessionDec 30, 2003ID: 1UIQ
Revision 1.0Dec 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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_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

Downloads & links

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Assembly

Deposited unit
A: THREONINE SYNTHASE
B: THREONINE SYNTHASE
C: THREONINE SYNTHASE
D: THREONINE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,9248
Polymers148,2194
Non-polymers1,7054
Water15,943885
1
A: THREONINE SYNTHASE
B: THREONINE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9624
Polymers74,1092
Non-polymers8532
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8460 Å2
ΔGint-57 kcal/mol
Surface area22530 Å2
MethodPISA
2
C: THREONINE SYNTHASE
D: THREONINE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9624
Polymers74,1092
Non-polymers8532
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8300 Å2
ΔGint-57 kcal/mol
Surface area22830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.586, 119.453, 123.418
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
THREONINE SYNTHASE /


Mass: 37054.656 Da / Num. of mol.: 4
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-HEY / (2E)-2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]-5-PHOSPHONOPENT-2-ENOIC ACID


Mass: 426.253 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H20N2O10P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 885 / 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: 2.69 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG8000, Calcium Acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1
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→20 Å / Num. all: 110109 / Num. obs: 110109 / % possible obs: 95 %
Reflection shellResolution: 2→2.07 Å / % possible all: 96.6

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Processing

Software
NameClassification
MOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→10 Å / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.23 10753 RANDOM
Rwork0.196 --
all-115646 -
obs-107545 -
Refine analyzeLuzzati coordinate error obs: 0.23 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10432 0 108 885 11425
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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