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Open data
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Basic information
Entry | Database: PDB / ID: 1jpm | ||||||
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Title | L-Ala-D/L-Glu Epimerase | ||||||
![]() | L-Ala-D/L-Glu Epimerase | ||||||
![]() | ISOMERASE / Enolase superfamily / muconate lactonizing subgroup / alpha-beta barrel | ||||||
Function / homology | ![]() L-Ala-D/L-Glu epimerase activity / L-Ala-D/L-Glu epimerase / cell wall organization / cell wall macromolecule catabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gulick, A.M. / Schmidt, D.M.Z. / Gerlt, J.A. / Rayment, I. | ||||||
![]() | ![]() Title: Evolution of enzymatic activities in the enolase superfamily: crystal structures of the L-Ala-D/L-Glu epimerases from Escherichia coli and Bacillus subtilis. Authors: Gulick, A.M. / Schmidt, D.M. / Gerlt, J.A. / Rayment, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 281.2 KB | Display | ![]() |
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PDB format | ![]() | 227.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.8 KB | Display | ![]() |
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Full document | ![]() | 477.1 KB | Display | |
Data in XML | ![]() | 54.5 KB | Display | |
Data in CIF | ![]() | 76.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 39519.582 Da / Num. of mol.: 4 / Fragment: L-Ala-D/L-Glu Epimerase Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.79 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.25 Details: 8% Peg400, 0.2M MgCl2,50 mM BisTRIS, pH 5.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5 | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Jun 1, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→30 Å / Num. all: 97105 / Num. obs: 97014 / % possible obs: 99 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 4.1 / Num. unique all: 9676 / % possible all: 99.9 |
Reflection | *PLUS % possible obs: 99.9 % / Num. measured all: 570691 |
Reflection shell | *PLUS % possible obs: 99.9 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 31.5 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.39 Å / Rfactor Rfree error: 0.01
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / σ(F): 0 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 31.5 Å2 | |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.276 / Rfactor Rwork: 0.232 / Rfactor obs: 0.232 |