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Yorodumi- PDB-1ub3: Crystal Structure of Tetrameric Structure of Aldolase from thermu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ub3 | ||||||
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Title | Crystal Structure of Tetrameric Structure of Aldolase from thermus thermophilus HB8 | ||||||
Components | Aldolase proteinFructose-bisphosphate aldolase | ||||||
Keywords | LYASE / Schiff base / deoxyribose phosphate / carbinolamine / STRUCTURAL GENOMICS / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information deoxyribose phosphate catabolic process / deoxyribose-phosphate aldolase / deoxyribose-phosphate aldolase activity / deoxyribonucleotide catabolic process / carbohydrate catabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å | ||||||
Authors | Lokanath, N.K. / Miyano, M. / Yokoyama, S. / Kuramitsu, S. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Structure of aldolase from Thermus thermophilus HB8 showing the contribution of oligomeric state to thermostability. Authors: Lokanath, N.K. / Shiromizu, I. / Ohshima, N. / Nodake, Y. / Sugahara, M. / Yokoyama, S. / Kuramitsu, S. / Miyano, M. / Kunishima, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ub3.cif.gz | 174.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ub3.ent.gz | 139.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ub3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ub/1ub3 ftp://data.pdbj.org/pub/pdb/validation_reports/ub/1ub3 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Molecule is in the tetramer form. The biological assempbly is a tetramer generated from the monomer in the asymmetric unit. |
-Components
#1: Protein | Mass: 23335.762 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: PET-11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: Q7SIC8, UniProt: Q5SJ28*PLUS, deoxyribose-phosphate aldolase #2: Chemical | ChemComp-HPD / #3: 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: 2.23 Å3/Da / Density % sol: 44.52 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 7.9 Details: MPD, Tris-HCl, MgCl2, Deoxyribose phosphate , pH 7.9, MICROBATCH, temperature 295.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.8 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Dec 8, 2002 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. all: 165080 / Num. obs: 164987 / % possible obs: 99.99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.046 |
Reflection shell | Resolution: 1.4→1.49 Å / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.4→29.25 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1106896.53 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.9881 Å2 / ksol: 0.402301 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.4→29.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.49 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
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Xplor file |
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