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Yorodumi- PDB-1rv8: Class II fructose-1,6-bisphosphate aldolase from Thermus aquaticu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rv8 | ||||||
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Title | Class II fructose-1,6-bisphosphate aldolase from Thermus aquaticus in complex with cobalt | ||||||
Components | fructose-1,6-bisphosphate aldolase | ||||||
Keywords | LYASE / class II aldolase / metal-depdendent aldolase | ||||||
Function / homology | Function and homology information tagatose-bisphosphate aldolase activity / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose 1,6-bisphosphate metabolic process / glycolytic process / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Thermus aquaticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Izard, T. / Sygusch, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Induced Fit Movements and Metal Cofactor Selectivity of Class II Aldolases: STRUCTURE OF THERMUS AQUATICUS FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE. Authors: Izard, T. / Sygusch, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rv8.cif.gz | 259.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rv8.ent.gz | 208.7 KB | Display | PDB format |
PDBx/mmJSON format | 1rv8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rv8_validation.pdf.gz | 404.4 KB | Display | wwPDB validaton report |
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Full document | 1rv8_full_validation.pdf.gz | 428 KB | Display | |
Data in XML | 1rv8_validation.xml.gz | 26.6 KB | Display | |
Data in CIF | 1rv8_validation.cif.gz | 44.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rv/1rv8 ftp://data.pdbj.org/pub/pdb/validation_reports/rv/1rv8 | 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: 33141.980 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus aquaticus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RHA2, fructose-bisphosphate aldolase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-CO / #4: Chemical | ChemComp-NA / #5: 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: 2.99 Å3/Da / Density % sol: 58.88 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 295 K / pH: 7.5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
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: NSLS / Beamline: X8C / Wavelength: 0.9791, 0.9783, 0.93, 1.105 | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→50 Å / Num. obs: 68760 / % possible obs: 97.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Biso Wilson estimate: 25.6 Å2 | |||||||||||||||
Reflection | *PLUS % possible obs: 97.7 % / Redundancy: 14.4 % / Num. measured all: 989324 / Rmerge(I) obs: 0.075 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 93.8 % / Rmerge(I) obs: 0.195 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→40.43 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1877215.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.4268 Å2 / ksol: 0.353232 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→40.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 40.4 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.3 Å / Rfactor Rfree: 0.303 |