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Yorodumi- PDB-5nd5: Crystal structure of transketolase from Chlamydomonas reinhardtii... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nd5 | ||||||
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Title | Crystal structure of transketolase from Chlamydomonas reinhardtii in complex with TPP and Mg2+ | ||||||
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: 1.74 Å | ||||||
Authors | Fermani, S. / Zaffagnini, M. / Francia, F. / Pasquini, M. | ||||||
Funding support | Italy, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nd5.cif.gz | 281.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nd5.ent.gz | 221.5 KB | Display | PDB format |
PDBx/mmJSON format | 5nd5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nd5_validation.pdf.gz | 1014.9 KB | Display | wwPDB validaton report |
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Full document | 5nd5_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5nd5_validation.xml.gz | 53.4 KB | Display | |
Data in CIF | 5nd5_validation.cif.gz | 78.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/5nd5 ftp://data.pdbj.org/pub/pdb/validation_reports/nd/5nd5 | HTTPS FTP |
-Related structure data
Related structure data | 5nd6C 1itzS 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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Unit cell |
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-Components
#1: Protein | Mass: 75266.641 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 | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.4 Å3/Da / Density % sol: 49 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 10, 2014 |
Radiation | Monochromator: Double Crystal Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→97.52 Å / Num. obs: 114961 / % possible obs: 76.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.74→1.82 Å / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.24 / % possible all: 64.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ITZ Resolution: 1.74→97.51 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.187 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.114 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.723 Å2
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Refinement step | Cycle: 1 / Resolution: 1.74→97.51 Å
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Refine LS restraints |
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