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- PDB-2c2g: Crystal structure of Threonine Synthase from Arabidopsis thaliana... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2c2g | ||||||
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Title | Crystal structure of Threonine Synthase from Arabidopsis thaliana in complex with its cofactor pyridoxal phosphate | ||||||
![]() | THREONINE SYNTHASE | ||||||
![]() | LYASE / SYNTHASE / THREONINE BIOSYNTHESIS / PYRIDOXAL PHOSPHATE / AMINO-ACID BIOSYNTHESIS | ||||||
Function / homology | ![]() threonine synthase / threonine synthase activity / threonine biosynthetic process / cysteine biosynthetic process / chloroplast stroma / chloroplast / pyridoxal phosphate binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Mas-Droux, C. / Biou, V. / Dumas, R. | ||||||
![]() | ![]() Title: Allosteric Threonine Synthase: Reorganization of the Pyridoxal Phosphate Site Upon Asymmetric Activation Through S-Adenosylmethionine Binding to a Novel Site. Authors: Mas-Droux, C. / Biou, V. / Dumas, R. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 183 KB | Display | ![]() |
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PDB format | ![]() | 144.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465 KB | Display | ![]() |
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Full document | ![]() | 498.5 KB | Display | |
Data in XML | ![]() | 37.8 KB | Display | |
Data in CIF | ![]() | 51.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2c2bC ![]() 1e5xS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 36 - 479 / Label seq-ID: 36 - 479
NCS oper: (Code: given Matrix: (0.93402, -0.16235, 0.31818), Vector: |
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Components
#1: Protein | Mass: 53385.590 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: RESIDUE 163 IS A LYSINE BOUND TO PYRIDOXAL PHOSPHATE VIA A SCHIFF BASE Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Compound details | HYDROLYSES O-PHOSPHO-L-HOMOSERINE INTO L-THREONINE AND PHOSPHATE. OTHER_DETAILS: RESIDUE 163 IS A ...HYDROLYSES | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 46.85 % |
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Crystal grow | pH: 6.5 Details: 1 M LICL, 13% (W/V) PEG 6000, 5 MM DTT, 0.1 M MES-KOH, pH 6.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 20, 2000 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. obs: 25774 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.61→2.75 Å / Redundancy: 2 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.5 / % possible all: 93.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1E5X Resolution: 2.61→20.63 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.898 / SU B: 27.272 / SU ML: 0.28 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R Free: 0.376 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-10 AND 347-362 IN MONOMER A, AND RESIDUES 1-20 AND 347-362 IN MONOMER B ARE DISORDERED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.61→20.63 Å
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Refine LS restraints |
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