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Yorodumi- PDB-2c2b: Crystallographic structure of Arabidopsis thaliana Threonine synt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c2b | ||||||
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Title | Crystallographic structure of Arabidopsis thaliana Threonine synthase complexed with pyridoxal phosphate and S-adenosylmethionine | ||||||
Components | THREONINE SYNTHASE 1, CHLOROPLASTIC | ||||||
Keywords | LYASE / THREONINE SYNTHESIS / ALLOSTERY / SYNTHASE | ||||||
Function / homology | Function and homology information threonine synthase / threonine synthase activity / threonine biosynthetic process / chloroplast stroma / chloroplast / pyridoxal phosphate binding / plasma membrane Similarity search - Function | ||||||
Biological species | ARABIDOPSIS THALIANA (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Mas-Droux, C. / Biou, V. / Dumas, R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c2b.cif.gz | 512.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c2b.ent.gz | 422.3 KB | Display | PDB format |
PDBx/mmJSON format | 2c2b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/2c2b ftp://data.pdbj.org/pub/pdb/validation_reports/c2/2c2b | HTTPS FTP |
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-Related structure data
Related structure data | 2c2gC 1e5xS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1
NCS ensembles :
NCS oper:
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Details | THE BIOLOGICAL UNIT OF ARABIDOPSIS THALIANA THREONINESYNTHASE (HOMODIMER) IN COMPLEX WITH SAM IS FORMED BY TWOASYMETRIC MONOMERS. IN ONE MONOMER THE ACTIVE SITECORRESPONDS TO AN INACTIVE FORM WHEREAS IN THE OTHERMONOMER, THE ACTIVE SITE CORRESPONDS TO AN ACTIVE FORM WITHA STANDARD PLP ORIENTATION FOR A TYPE II FAMILY PLPENZYMES. |
-Components
#1: Protein | Mass: 53385.590 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PET23D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9S7B5, threonine synthase #2: Chemical | ChemComp-SAM / #3: Chemical | #4: Chemical | ChemComp-PLP / #5: Water | ChemComp-HOH / | Sequence details | THIS SEQUENCE CORRESPOND | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.3 Å3/Da / Density % sol: 76.4 % |
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Crystal grow | pH: 6.5 Details: 10 MM CACL2, 15% (W/V) PEG 2000 MONOMETHYL ETHER, 1 MM PLP, 5MM SAM, 100 MM BISTRIS PH 6.5 BUFFER |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 30, 2004 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 93317 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E5X Resolution: 2.6→29.89 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.922 / SU B: 25.549 / SU ML: 0.272 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.812 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-35 AND 480-486 ARE DISORDERED IN MONOMERS A, C AND F RESIDUS 1-34, 344-362 AND 482-486 ARE DISORDERED IN MONOMERS B, D AND E.
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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: 60.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→29.89 Å
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Refine LS restraints |
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