[English] 日本語
Yorodumi- PDB-5nd6: Crystal structure of apo transketolase from Chlamydomonas reinhardtii -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nd6 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of apo transketolase from Chlamydomonas reinhardtii | ||||||
Components | Transketolase | ||||||
Keywords | TRANSFERASE / Calvin-Benson cycle / thiamine pyrophosphate / Magnesium-dependent activation | ||||||
Function / homology | Function and homology information transketolase / transketolase activity / pentose-phosphate shunt / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Chlamydomonas reinhardtii (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Fermani, S. / Zaffagnini, M. / Francia, F. / Pasquini, M. | ||||||
Funding support | Italy, 1items
| ||||||
Citation | Journal: Biochim. Biophys. Acta / Year: 2017 Title: Structural basis for the magnesium-dependent activation of transketolase from Chlamydomonas reinhardtii. Authors: Pasquini, M. / Fermani, S. / Tedesco, D. / Sciabolini, C. / Crozet, P. / Naldi, M. / Henri, J. / Vothknecht, U. / Bertucci, C. / Lemaire, S.D. / Zaffagnini, M. / Francia, F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5nd6.cif.gz | 281.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5nd6.ent.gz | 223.6 KB | Display | PDB format |
PDBx/mmJSON format | 5nd6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/5nd6 ftp://data.pdbj.org/pub/pdb/validation_reports/nd/5nd6 | HTTPS FTP |
---|
-Related structure data
Related structure data | 5nd5C 1itzS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 75337.719 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: TRK1, CHLREDRAFT_141319 / Organ: Chloroplast / Plasmid: pET-3c / Production host: Escherichia coli (E. coli) / References: UniProt: A8IAN1, transketolase #2: Chemical | ChemComp-EDO / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 47 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 10 % w/v PEG 6K, 5 % v/v MPD and 0.1 M MES pH 6.5-7.0 or 0.1 M HEPES pH 7.0-8.0. PH range: 6.5-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.912 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 9, 2016 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.912 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→116.6 Å / Num. obs: 193102 / % possible obs: 98.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.58→1.64 Å / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.567 / % possible all: 97.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ITZ Resolution: 1.58→116.6 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.027 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.077 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.221 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.58→116.6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|