[English] 日本語
Yorodumi- PDB-4d2j: Crystal structure of F16BP Aldolase from Toxoplasma gondii (TgALD1) -
+Open data
-Basic information
Entry | Database: PDB / ID: 4d2j | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of F16BP Aldolase from Toxoplasma gondii (TgALD1) | ||||||
Components | FRUCTOSE-BISPHOSPHATE ALDOLASE | ||||||
Keywords | LYASE / APICOMPLEXA / TIM BARREL / GLYCOLYSIS | ||||||
Function / homology | Function and homology information apical cytoplasm / biological process involved in symbiotic interaction / adhesion of symbiont to host cell / symbiont entry into host / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose 1,6-bisphosphate metabolic process / positive regulation of ATP biosynthetic process / glycolytic process / actin filament binding ...apical cytoplasm / biological process involved in symbiotic interaction / adhesion of symbiont to host cell / symbiont entry into host / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose 1,6-bisphosphate metabolic process / positive regulation of ATP biosynthetic process / glycolytic process / actin filament binding / membrane => GO:0016020 / positive regulation of cell population proliferation / extracellular space / membrane Similarity search - Function | ||||||
Biological species | TOXOPLASMA GONDII (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Tonkin, M.L. / Ramaswamy, R. / Halavaty, A.S. / Ruan, J. / Igarashi, M. / Ngo, H.M. / Boulanger, M.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2015 Title: Structural and Functional Divergence of the Aldolase Fold in Toxoplasma Gondii. Authors: Tonkin, M.L. / Halavaty, A.S. / Ramaswamy, R. / Ruan, J. / Igarashi, M. / Ngo, H.M. / Boulanger, M.J. | ||||||
History |
| ||||||
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 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4d2j.cif.gz | 84.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4d2j.ent.gz | 61.4 KB | Display | PDB format |
PDBx/mmJSON format | 4d2j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4d2j_validation.pdf.gz | 467.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4d2j_full_validation.pdf.gz | 469.9 KB | Display | |
Data in XML | 4d2j_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 4d2j_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/4d2j ftp://data.pdbj.org/pub/pdb/validation_reports/d2/4d2j | HTTPS FTP |
-Related structure data
Related structure data | 3qyqC 4eivC 3kx6S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37822.301 Da / Num. of mol.: 1 / Fragment: F16BP ALDOLASE, RESIDUES 7-422 Source method: isolated from a genetically manipulated source Source: (gene. exp.) TOXOPLASMA GONDII (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: S8GE25, UniProt: B9PW35*PLUS, fructose-bisphosphate aldolase |
---|
-Non-polymers , 5 types, 191 molecules
#2: Chemical | ChemComp-BME / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.33 % / Description: NONE |
---|---|
Crystal grow | pH: 7.5 Details: 0.1 M SODIUM CHLORIDE, 0.1 M HEPES PH 7.5, 1.6 M AMMONIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 33917 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 13.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 44 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 4 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3KX6 Resolution: 1.75→36.44 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.866 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.612 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→36.44 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|