+Open data
-Basic information
Entry | Database: PDB / ID: 1wx0 | ||||||
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Title | Crystal structure of transaldolase from Thermus thermophilus HB8 | ||||||
Components | transaldolase | ||||||
Keywords | TRANSFERASE / structural genomics / Thermus thermophilus HB8 / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information transaldolase / transaldolase activity / aldehyde-lyase activity / pentose-phosphate shunt / carbohydrate metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus HB8 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å | ||||||
Authors | Asada, Y. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of transaldolase from Thermus thermophilus HB8 Authors: Asada, Y. / Kunishima, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wx0.cif.gz | 413.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wx0.ent.gz | 338.9 KB | Display | PDB format |
PDBx/mmJSON format | 1wx0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wx/1wx0 ftp://data.pdbj.org/pub/pdb/validation_reports/wx/1wx0 | HTTPS FTP |
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-Related structure data
Related structure data | 1l6wS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is decamer |
-Components
#1: Protein | Mass: 24051.885 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Species: Thermus thermophilus / Strain: HB8 / ATCC 27634 / DSM 579 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SJE8, transaldolase #2: 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: 2.44 Å3/Da / Density % sol: 49.67 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 8.5 Details: Magnesium Chloride, Tris Hydrochloride, PEG 4000, Glycerol, pH 8.5, MICROBATCH, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Oct 22, 2003 / Details: mirrors |
Radiation | Monochromator: Bending Magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→30 Å / Num. all: 105189 / Num. obs: 105189 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 37.36 Å2 / Rmerge(I) obs: 0.108 / Rsym value: 0.096 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.27→2.35 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 3.59 / Num. unique all: 10402 / Rsym value: 0.466 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1L6W.pdb Resolution: 2.27→29.6 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 41.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.27→29.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.27→2.37 Å / Rfactor Rfree error: 0.011
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