+Open data
-Basic information
Entry | Database: PDB / ID: 1j2w | ||||||
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Title | Tetrameric Structure of aldolase from Thermus thermophilus HB8 | ||||||
Components | Aldolase proteinFructose-bisphosphate aldolase | ||||||
Keywords | LYASE / Schiff base / deoxyribose phospahte / 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 / MAD / Resolution: 1.5 Å | ||||||
Authors | Lokanath, N.K. / Shiromizu, I. / 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 | 1j2w.cif.gz | 170.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j2w.ent.gz | 137.2 KB | Display | PDB format |
PDBx/mmJSON format | 1j2w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j2/1j2w ftp://data.pdbj.org/pub/pdb/validation_reports/j2/1j2w | 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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-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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7SIC8, UniProt: Q5SJ28*PLUS #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: 2.27 Å3/Da / Density % sol: 45.34 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 7.9 Details: MPD, Tris HCl, magnesium chloride, pH 7.9, MICROBATCH, temperature 295.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 4.9 / Method: batch method | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-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: Nov 25, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. all: 137192 / Num. obs: 137075 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 14.62 Å2 |
Reflection shell | Resolution: 1.5→1.55 Å / % possible all: 99.5 |
Reflection | *PLUS Highest resolution: 1.5 Å / Num. obs: 137192 / % possible obs: 98.5 % / Redundancy: 4.85 % / Num. measured all: 665297 / Rmerge(I) obs: 0.067 |
Reflection shell | *PLUS Highest resolution: 1.5 Å / % possible obs: 99.5 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 4.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.5→30 Å / Isotropic thermal model: ANISOTROPIC / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.5→30 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.5 Å / Rfactor Rwork: 0.196 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.29 |