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Yorodumi- PDB-1ehi: D-ALANINE:D-LACTATE LIGASE (LMDDL2) OF VANCOMYCIN-RESISTANT LEUCO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ehi | ||||||
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Title | D-ALANINE:D-LACTATE LIGASE (LMDDL2) OF VANCOMYCIN-RESISTANT LEUCONOSTOC MESENTEROIDES | ||||||
Components | D-ALANINE:D-LACTATE LIGASE | ||||||
Keywords | LIGASE / ATP-binding. Grasp motif for ATP. | ||||||
Function / homology | Function and homology information D-alanine-D-alanine ligase / D-alanine-D-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Leuconostoc mesenteroides (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / 3-wavelength MAD near Se edge (x12c at BNL) / Resolution: 2.38 Å | ||||||
Authors | Kuzin, A.P. / Sun, T. / Jorczak-Baillass, J. / Healy, V.L. / Walsh, C.T. / Knox, J.R. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 2000 Title: Enzymes of vancomycin resistance: the structure of D-alanine-D-lactate ligase of naturally resistant Leuconostoc mesenteroides. Authors: Kuzin, A.P. / Sun, T. / Jorczak-Baillass, J. / Healy, V.L. / Walsh, C.T. / Knox, J.R. #1: Journal: Science / Year: 1994 Title: Vancomycin Resistance: Structure of D-alanine:D-alanine Ligase at 2.3 A Resolution Authors: Fan, C. / Moews, P.C. / Walsh, C.T. / Knox, J.R. #2: Journal: Biochemistry / Year: 1997 Title: D-alanine:D-alanine ligase: Phosphonate and Phosphinate Intermediates with Wild-type and the Y216F Mutant Authors: Fan, C. / Park, I.-S. / Walsh, C.T. / Knox, J.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ehi.cif.gz | 156.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ehi.ent.gz | 122.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ehi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eh/1ehi ftp://data.pdbj.org/pub/pdb/validation_reports/eh/1ehi | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The ligase is a dimer formed of chain A and B. However, part of chain B is missing in the crystallographic model. |
-Components
#1: Protein | Mass: 41866.883 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leuconostoc mesenteroides (bacteria) / Plasmid: PLMDDL2 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5A AND BL21(DE3) References: UniProt: P71454, UniProt: Q03ZI1*PLUS, D-alanine-D-alanine ligase #2: Chemical | #3: Chemical | ChemComp-ADP / | #4: Chemical | ChemComp-PHY / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53.2 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG8000 15%, 0.1 M ammonium sulfate, 50mM NaCl, 2.4mM DTT, 1mM MgCl2, 3mM ATP, 3mM phosphinic acid, 50mM MES buffer., pH 6.5, VAPOR DIFFUSION, SITTING DROP Temp details: 293-295 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908 |
Detector | Type: ADSC / Detector: CCD / Date: Aug 15, 1997 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.908 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→100 Å / Num. all: 30564 / Num. obs: 30564 / % possible obs: 82 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.38→2.48 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1738 / % possible all: 47 |
Reflection | *PLUS % possible obs: 82 % / Num. measured all: 94338 |
Reflection shell | *PLUS % possible obs: 47 % / Num. unique obs: 1738 / Num. measured obs: 4374 |
-Processing
Software |
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Refinement | Method to determine structure: 3-wavelength MAD near Se edge (x12c at BNL) Resolution: 2.38→100 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: bulk solvent correction. A 3-wavelength MAD method was used to determine structure of the selenomet-protein. A native data set (A1 at CHESS) was used to refine structure.
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Refinement step | Cycle: LAST / Resolution: 2.38→100 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 100 Å / σ(F): 0 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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