+Open data
-Basic information
Entry | Database: PDB / ID: 2pty | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the T. brucei enolase complexed with PEP | ||||||
Components | Enolase | ||||||
Keywords | LYASE / GLYCOLYSIS / HIS-TAG | ||||||
Function / homology | Function and homology information phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / ciliary plasm / glycolytic process / magnesium ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Trypanosoma brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Navarro, M.V.A.S. / Rigden, D.J. / Garratt, R.C. / Dias, S.M.G. | ||||||
Citation | Journal: Febs J. / Year: 2007 Title: Structural flexibility in Trypanosoma brucei enolase revealed by X-ray crystallography and molecular dynamics. Authors: Navarro, M.V. / Gomes Dias, S.M. / Mello, L.V. / da Silva Giotto, M.T. / Gavalda, S. / Blonski, C. / Garratt, R.C. / Rigden, D.J. #1: Journal: J.Mol.Biol. / Year: 2003 Title: The Crystal Structure of Trypanosoma Brucei Enolase: Visualisation of the Inhibitory Metal Binding Site III and Potential as Target for Selective, Irreversible Inhibition Authors: da Silva Giotto, M.T. / Hannaert, V. / Vertommen, D. / Navarro, M.V.A.S. / Rider, M.H. / Michels, P.A.M. / Garratt, R.C. / Rigden, D.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2pty.cif.gz | 188.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2pty.ent.gz | 148.3 KB | Display | PDB format |
PDBx/mmJSON format | 2pty.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pt/2pty ftp://data.pdbj.org/pub/pdb/validation_reports/pt/2pty | HTTPS FTP |
---|
-Related structure data
Related structure data | 2ptwC 2ptxC 2ptzC 2pu0C 2pu1C 1oepS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a dimer generated from the monomer in the asymmetric unit by the operations: -x, y, -z+1/2 |
-Components
#1: Protein | Mass: 46904.434 Da / Num. of mol.: 1 / Mutation: R28K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q38BV6, phosphopyruvate hydratase | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-PEP / | #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.44 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10 % (w/v) PEG1000, 0.01 M ZnSO4 or ZnCl2, and 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 7, 2004 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. all: 30574 / Num. obs: 30513 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 1.9 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OEP Resolution: 2→24.98 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / SU B: 9.895 / SU ML: 0.122 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.159 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.237 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→24.98 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.107 Å / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|