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Yorodumi- PDB-1w8s: The mechanism of the Schiff Base Forming Fructose-1,6-bisphosphat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w8s | ||||||
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Title | The mechanism of the Schiff Base Forming Fructose-1,6-bisphosphate Aldolase: Structural analysis of reaction intermediates | ||||||
Components | FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I | ||||||
Keywords | LYASE / ALDOLASE / FRUCTOSE 1 / 6-BISPHOSPHATE / TIM BARREL / GLYCOLYTIC / ARCHAEAL / CATALYTIC MECHANISM / REACTION INTERMEDIATE | ||||||
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: 1.85 Å | ||||||
Authors | Lorentzen, E. / Hensel, R. / Siebers, B. / Pohl, E. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Mechanism of the Schiff base forming fructose-1,6-bisphosphate aldolase: structural analysis of reaction intermediates. Authors: Lorentzen, E. / Siebers, B. / Hensel, R. / Pohl, E. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA, BA, CA" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA, BA, CA" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY 9-STRANDED BARRELS WHICH ARE REPRESENTED BY 10-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "DA, EA, FA, GA, HA, IA, JA" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY 7-STRANDED BARRELS REPRESENTED BY 8-STRANDED SHEETS 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 | 1w8s.cif.gz | 498.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w8s.ent.gz | 413 KB | Display | PDB format |
PDBx/mmJSON format | 1w8s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/1w8s ftp://data.pdbj.org/pub/pdb/validation_reports/w8/1w8s | HTTPS FTP |
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-Related structure data
Related structure data | 2yceC 1ojxS 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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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.96895, -0.16745, -0.18194), Vector: |
-Components
#1: Protein | Mass: 28667.971 Da / Num. of mol.: 10 / Mutation: YES Source method: isolated from a genetically manipulated source Details: CYCLIC FBP BOUND / Source: (gene. exp.) THERMOPROTEUS TENAX (archaea) / Plasmid: PET15B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P58315, fructose-bisphosphate aldolase #2: Sugar | ChemComp-FBP / #3: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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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: 2.3 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, 100 MM FBP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.842 |
Detector | Date: Nov 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.842 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→40 Å / Num. obs: 199708 / % possible obs: 100 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 1.85→1.86 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 2.2 / % possible all: 60 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OJX Resolution: 1.85→40 Å / SU B: 2.759 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.115 Details: DEFAULT REFMAC5 BULK SOLVENT MODELLING. RESIDUES 1-2 AND 153-263 DISORDERED AND NOT MODELLED.
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Displacement parameters | Biso mean: 14.875 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→40 Å
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