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Yorodumi- PDB-2yce: Structure of an Archaeal fructose-1,6-bisphosphate aldolase with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yce | |||||||||
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Title | Structure of an Archaeal fructose-1,6-bisphosphate aldolase with the catalytic Lys covalently bound to the carbinolamine intermediate of the substrate. | |||||||||
Components | FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1 | |||||||||
Keywords | LYASE / GLYCOLYSIS | |||||||||
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: 1.93 Å | |||||||||
Authors | Lorentzen, E. / Siebers, B. / Hensel, R. / 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yce.cif.gz | 974.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yce.ent.gz | 818.2 KB | Display | PDB format |
PDBx/mmJSON format | 2yce.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/2yce ftp://data.pdbj.org/pub/pdb/validation_reports/yc/2yce | HTTPS FTP |
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-Related structure data
Related structure data | 1w8sC 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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-Components
#1: Protein | Mass: 28741.064 Da / Num. of mol.: 10 / Mutation: YES Source method: isolated from a genetically manipulated source Details: K177 COVALENTLY LINKED TO THE CARBINOLAMINE FORM OF THE SUBSTRATE FBP Source: (gene. exp.) THERMOPROTEUS TENAX (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P58315, fructose-bisphosphate aldolase #2: Chemical | ChemComp-M2P / #3: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, TYR 146 TO PHE ENGINEERED RESIDUE IN CHAIN A, ALA 173 TO SER ...ENGINEERED | Nonpolymer details | M2P: THE SUBSTRATE FRUCTOSE 1,6-BISPHOSPHATE IS COVALENTLY LINKED TO THE CATALYTIC LYSINE AS A ...M2P: THE SUBSTRATE 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 Å3/Da / Density % sol: 40 % / Description: SOLVED BY RIGID BODY REFINEMENT OF 1OJX. |
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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: X11 / Wavelength: 0.812 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.812 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→40 Å / Num. obs: 179009 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.93→2.02 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.2 / % possible all: 77.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OJX Resolution: 1.93→39.8 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.061 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.83 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→39.8 Å
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Refine LS restraints |
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