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Yorodumi- PDB-1ok6: Orthorhombic crystal form of an Archaeal fructose 1,6-bisphosphat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ok6 | ||||||
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Title | Orthorhombic crystal form 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 / ORTHORHOMBIC / SCHIFF BASE | ||||||
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: 2.4 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" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" 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. THE SHEETS PRESENTED AS "BA" 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. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "HA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "IA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "JA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-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 | 1ok6.cif.gz | 483.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ok6.ent.gz | 400.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ok6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ok6_validation.pdf.gz | 517.4 KB | Display | wwPDB validaton report |
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Full document | 1ok6_full_validation.pdf.gz | 550.8 KB | Display | |
Data in XML | 1ok6_validation.xml.gz | 95.2 KB | Display | |
Data in CIF | 1ok6_validation.cif.gz | 130.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/1ok6 ftp://data.pdbj.org/pub/pdb/validation_reports/ok/1ok6 | HTTPS FTP |
-Related structure data
Related structure data | 1ojxSC 1ok4C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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: Chemical | ChemComp-GOL / | #3: Water | ChemComp-HOH / | Compound details | CATALYTIC ACTIVITY: D-FRUCTOSE 1,6-BISPHOSPHA | |
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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: 2.6 Å3/Da / Density % sol: 53 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5 / Details: 9% (W/V) PEG 4000, 0.1 M NA ACETATE PH 5.0 | |||||||||||||||||||||||||||||||||||||||||||||||||
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: BW7B / 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: 2.39→20 Å / Num. obs: 106518 / % possible obs: 93.6 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.39→2.47 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 2.7 / % possible all: 69 |
Reflection | *PLUS Highest resolution: 2.39 Å / Lowest resolution: 20 Å / Rmerge(I) obs: 0.121 |
Reflection shell | *PLUS % possible obs: 69 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 2.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OJX Resolution: 2.4→20 Å / SU B: 7.96 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.494 / ESU R Free: 0.277
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Displacement parameters | Biso mean: 32.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refinement | *PLUS Highest resolution: 2.39 Å / Num. reflection Rfree: 2735 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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