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Open data
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Basic information
Entry | Database: PDB / ID: 1e4e | ||||||
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Title | D-alanyl-D-lacate ligase | ||||||
![]() | (VANCOMYCIN/TEICOPLANIN A-TYPE RESISTANCE PROTEIN ...) x 2 | ||||||
![]() | LIGASE / CELL WALL / ANTIBIOTIC RESISTANCE / MEMBRANE / PEPTIDOGLYCAN SYNTHESIS | ||||||
Function / homology | ![]() D-alanine-(R)-lactate ligase / D-alanine-D-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic / ATP binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Roper, D.I. | ||||||
![]() | ![]() Title: The molecular basis of vancomycin resistance in clinically relevant Enterococci: crystal structure of D-alanyl-D-lactate ligase (VanA). Authors: Roper, D.I. / Huyton, T. / Vagin, A. / Dodson, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 160.5 KB | Display | ![]() |
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PDB format | ![]() | 123.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 37.8 KB | Display | |
Data in CIF | ![]() | 51.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1iowS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.57983, -0.49666, -0.64586), Vector: |
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Components
-VANCOMYCIN/TEICOPLANIN A-TYPE RESISTANCE PROTEIN ... , 2 types, 2 molecules AB
#1: Protein | Mass: 37575.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 37618.141 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 6 types, 380 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/PHY.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PHY.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MG / #6: Chemical | #7: Chemical | ChemComp-GOL / #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | CHAIN A AND CHAIN B DIFFER AT RESIDUE 298 |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.13 % | ||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 / Details: pH 6.50 | ||||||||||||||||||
Crystal grow | *PLUS pH: 6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() |
Detector | Date: Jan 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→15 Å / Num. obs: 32814 / % possible obs: 93.3 % / Observed criterion σ(I): 2 / Redundancy: 1 % / Biso Wilson estimate: 41.66 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 29.9 |
Reflection shell | Resolution: 2.5→2.54 Å / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 4.1 / % possible all: 96.6 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / % possible obs: 96.6 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 4.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1IOW Resolution: 2.5→15 Å / SU B: 0.191 / SU ML: 0.189 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.39 / ESU R Free: 0.29
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Displacement parameters | Biso mean: 44.8 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→15 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 15 Å / Rfactor obs: 0.183 / Rfactor Rfree: 0.284 / Rfactor Rwork: 0.205 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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