+Open data
-Basic information
Entry | Database: PDB / ID: 1jpd | ||||||
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Title | L-Ala-D/L-Glu Epimerase | ||||||
Components | L-Ala-D/L-Glu Epimerase | ||||||
Keywords | ISOMERASE / Enolase Superfamily / Muconate lactonizing enzyme subgroup / alpha/beta barrel / structural genomics | ||||||
Function / homology | Function and homology information L-Ala-D/L-Glu epimerase / racemase and epimerase activity, acting on amino acids and derivatives / peptidoglycan turnover / amino acid catabolic process / cell wall organization / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å | ||||||
Authors | Gulick, A.M. / Schmidt, D.M.Z. / Gerlt, J.A. / Rayment, I. | ||||||
Citation | Journal: Biochemistry / Year: 2001 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jpd.cif.gz | 74.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jpd.ent.gz | 55.2 KB | Display | PDB format |
PDBx/mmJSON format | 1jpd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jp/1jpd ftp://data.pdbj.org/pub/pdb/validation_reports/jp/1jpd | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34989.176 Da / Num. of mol.: 1 / Mutation: Tripeptide linker Gly-Ser-His Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P51981, EC: 5.5.-.- |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.02 Å3/Da / Density % sol: 69.42 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 400-500mM NaCl, 50 mM Succinate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.70008 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Dec 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.70008 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. all: 18206 / Num. obs: 17409 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 60.4 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 9.1 / % possible all: 97 |
Reflection | *PLUS Num. obs: 17379 / Num. measured all: 101261 |
Reflection shell | *PLUS % possible obs: 97 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.6→20.4 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→20.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.027
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 20.4 Å / σ(F): 0 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 2.76 Å / Rfactor Rfree: 0.338 / Rfactor Rwork: 0.3 / Rfactor obs: 0.3 |