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Yorodumi- PDB-1ojx: Crystal structure of an Archaeal fructose 1,6-bisphosphate aldolase -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ojx | ||||||
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Title | Crystal structure of an Archaeal fructose 1,6-bisphosphate aldolase | ||||||
Components | FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I | ||||||
Keywords | LYASE / ALDOLASE / FRUCTOSE 1 / 6-BISPHOSPHATE / TIM BARREL / GLYCOLYTIC / ARCHAEAL | ||||||
Function / homology | Function and homology information fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / glycolytic process / cytoplasm Similarity search - Function | ||||||
Biological species | THERMOPROTEUS TENAX (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Lorentzen, E. / Zwart, P. / Stark, A. / Hensel, R. / Siebers, B. / Pohl, E. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2003 Title: Crystal structure of an archaeal class I aldolase and the evolution of (betaalpha)8 barrel proteins. Authors: Lorentzen, E. / Pohl, E. / Zwart, P. / Stark, A. / Russell, R.B. / Knura, T. / Hensel, R. / Siebers, B. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA, BA, CA, DA, EA, FA, GA, HA, IA, JA" ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA, BA, CA, DA, EA, FA, GA, HA, IA, JA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ojx.cif.gz | 506.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ojx.ent.gz | 432.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ojx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/1ojx ftp://data.pdbj.org/pub/pdb/validation_reports/oj/1ojx | HTTPS FTP |
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-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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 28741.064 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOPROTEUS TENAX (archaea) / Plasmid: PET15B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P58315, fructose-bisphosphate aldolase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 45 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5 Details: 9% (W/V) PEG 4000, 0.1 M NAACETATE PH 5.0, 1-8% GLYCEROL | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging 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: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.845 |
Detector | Date: Feb 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.845 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. obs: 188245 / % possible obs: 94.5 % / Redundancy: 4 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 2.4 / % possible all: 87 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 40 Å / Rmerge(I) obs: 0.085 |
Reflection shell | *PLUS % possible obs: 87 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 2.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→40 Å / SU B: 2.776 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.118 / Details: DEFAULT REFMAC5 BULK SOLVENT MODELLING
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Displacement parameters | Biso mean: 13.234 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→40 Å
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Refinement | *PLUS Highest resolution: 1.9 Å / Num. reflection obs: 183520 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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