+Open data
-Basic information
Entry | Database: PDB / ID: 1epx | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE ANALYSIS OF ALDOLASE FROM L. MEXICANA | ||||||
Components | FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE | ||||||
Keywords | LYASE / beta barrel / pts signal / aldolase / leishmania / fructose-1 / 6-bisphosphate | ||||||
Function / homology | Function and homology information fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose 1,6-bisphosphate metabolic process / glycolytic process / cytosol Similarity search - Function | ||||||
Biological species | Leishmania mexicana (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Chudzik, D.M. / Michels, P.A. / de Walque, S. / Hol, W.G.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Structures of type 2 peroxisomal targeting signals in two trypanosomatid aldolases. Authors: Chudzik, D.M. / Michels, P.A. / de Walque, S. / Hol, W.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1epx.cif.gz | 306.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1epx.ent.gz | 245.1 KB | Display | PDB format |
PDBx/mmJSON format | 1epx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1epx_validation.pdf.gz | 389.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1epx_full_validation.pdf.gz | 432.3 KB | Display | |
Data in XML | 1epx_validation.xml.gz | 32.8 KB | Display | |
Data in CIF | 1epx_validation.cif.gz | 50.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/1epx ftp://data.pdbj.org/pub/pdb/validation_reports/ep/1epx | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 40723.539 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania mexicana (eukaryote) / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 PLYSS / References: UniProt: Q9U5N6, fructose-bisphosphate aldolase #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 50.42 % | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 13% mmePEG 5000, 50 mM sodium phosphate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K | |||||||||||||||
Crystal grow | *PLUS | |||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 150 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 18, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 139248 / Num. obs: 515238 / % possible obs: 92.9 % / Observed criterion σ(F): 20 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 14.95 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 18.53 |
Reflection shell | Resolution: 1.8→1.88 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.087 / Num. unique all: 45455 / % possible all: 55 |
Reflection | *PLUS Num. obs: 139238 / Num. measured all: 515238 |
Reflection shell | *PLUS % possible obs: 55 % |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: T. Brucei Aldolase Resolution: 1.8→20 Å / σ(F): 10000000 / σ(I): 2 / Stereochemistry target values: TNT ideal values
| |||||||||||||||||||||||||
Solvent computation | Solvent model: Babinet Method / Bsol: 228.441 Å2 / ksol: 0.80209 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.5 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Refine LS restraints NCS | Weight Biso : 2 / Weight position: 300 | |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.83 Å / Total num. of bins used: 8
| |||||||||||||||||||||||||
Xplor file | Serial no: 1 / Param file: protein_rep.param / Topol file: water.param | |||||||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.22 / Rfactor Rwork: 0.165 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |