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Yorodumi- PDB-2xmp: Crystal structure of trehalose synthase TreT mutant E326A from P.... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xmp | ||||||
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Title | Crystal structure of trehalose synthase TreT mutant E326A from P. horishiki in complex with UDP | ||||||
Components | TREHALOSE-SYNTHASE TRET | ||||||
Keywords | SUGAR BINDING PROTEIN | ||||||
Function / homology | Function and homology information alpha,alpha-trehalose synthase / trehalose synthase activity / glucose metabolic process Similarity search - Function | ||||||
Biological species | PYROCOCCUS HORIKOSHII (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Song, H.-N. / Jung, T.-Y. / Yoon, S.-M. / Lee, S.-B. / Lim, M.-Y. / Woo, E.-J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Structural Insights on the New Mechanism of Trehalose Synthesis by Trehalose Synthase Tret from Pyrococcus Horikoshii. Authors: Woo, E.-J. / Ryu, S. / Song, H.-N. / Jung, T.-Y. / Yeon, S. / Lee, H. / Park, B.C. / Park, K. / Lee, S.-B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xmp.cif.gz | 180.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xmp.ent.gz | 145.1 KB | Display | PDB format |
PDBx/mmJSON format | 2xmp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xmp_validation.pdf.gz | 962.8 KB | Display | wwPDB validaton report |
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Full document | 2xmp_full_validation.pdf.gz | 1000 KB | Display | |
Data in XML | 2xmp_validation.xml.gz | 36.8 KB | Display | |
Data in CIF | 2xmp_validation.cif.gz | 49.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xm/2xmp ftp://data.pdbj.org/pub/pdb/validation_reports/xm/2xmp | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 48179.516 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) PYROCOCCUS HORIKOSHII (archaea) / Plasmid: P6XHIS119 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): MC1061 / References: UniProt: O58762 #2: Chemical | #3: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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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: 2.29 Å3/Da / Density % sol: 54 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 25% PEG3350,0.2M MGCL2,0.1M SODIUM HEPES BUFFER,5MM UDP, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 297 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1.2399 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 1, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2399 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→2.59 Å / Num. obs: 26469 / % possible obs: 80.9 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.59→30 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.85 / % possible all: 62.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→29.31 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 78598.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.3375 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→29.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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