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- PDB-2y4a: Unexpected tricovalent binding mode of boronic acids within the a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2y4a | ||||||
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Title | Unexpected tricovalent binding mode of boronic acids within the active site of a penicillin binding protein | ||||||
![]() | D-ALANYL-D-ALANINE CARBOXYPEPTIDASE | ||||||
![]() | HYDROLASE / PEPTIDOGLYCAN / TETRAVALENT BORON | ||||||
Function / homology | ![]() serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sauvage, E. / Zervosen, A. / Herman, R. / Kerff, F. / Rocaboy, M. / Charlier, P. | ||||||
![]() | ![]() Title: Unexpected Tricovalent Binding Mode of Boronic Acids within the Active Site of a Penicillin- Binding Protein. Authors: Zervosen, A. / Herman, R. / Kerff, F. / Herman, A. / Bouillez, A. / Prati, F. / Pratt, R.F. / Frere, J.M. / Joris, B. / Luxen, A. / Charlier, P. / Sauvage, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 668.4 KB | Display | ![]() |
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PDB format | ![]() | 558.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 492.6 KB | Display | ![]() |
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Full document | ![]() | 517.8 KB | Display | |
Data in XML | ![]() | 64.8 KB | Display | |
Data in CIF | ![]() | 88.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2y55C ![]() 2y59C ![]() 3zvtC ![]() 3zvwC ![]() 2xdmS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 47647.004 Da / Num. of mol.: 4 / Fragment: RESIDUES 50-515 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P39045, serine-type D-Ala-D-Ala carboxypeptidase #2: Chemical | ChemComp-BH6 / {[( #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.5 % / Description: NONE |
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Crystal grow | pH: 6 / Details: pH 6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Date: Jan 31, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0724 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→46.1 Å / Num. obs: 53645 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.8 / % possible all: 97.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2XDM Resolution: 2.7→46.1 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.911 / SU B: 25.52 / SU ML: 0.294 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 47.5 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→46.1 Å
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Refine LS restraints |
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