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Yorodumi- PDB-2y59: Unexpected tricovalent binding mode of boronic acids within the a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y59 | ||||||
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Title | Unexpected tricovalent binding mode of boronic acids within the active site of a penicillin binding protein | ||||||
Components | D-ALANYL-D-ALANINE CARBOXYPEPTIDASE | ||||||
Keywords | HYDROLASE / HYDROLASE-INHIBITOR COMPLEX / PEPTIDOGLYCAN | ||||||
Function / homology | Function and homology information 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 | ACTINOMADURA SP. R39 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Sauvage, E. / Zervosen, A. / Herman, R. / Kerff, F. / Rocaboy, M. / Charlier, P. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y59.cif.gz | 677.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y59.ent.gz | 565.3 KB | Display | PDB format |
PDBx/mmJSON format | 2y59.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2y59_validation.pdf.gz | 493.4 KB | Display | wwPDB validaton report |
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Full document | 2y59_full_validation.pdf.gz | 519.8 KB | Display | |
Data in XML | 2y59_validation.xml.gz | 68.8 KB | Display | |
Data in CIF | 2y59_validation.cif.gz | 95.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y5/2y59 ftp://data.pdbj.org/pub/pdb/validation_reports/y5/2y59 | HTTPS FTP |
-Related structure data
Related structure data | 2y4aC 2y55C 3zvtC 3zvwC 2xdmS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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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 / Source method: isolated from a natural source / Source: (natural) ACTINOMADURA SP. R39 (bacteria) References: UniProt: P39045, serine-type D-Ala-D-Ala carboxypeptidase #2: Chemical | ChemComp-ZA3 / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | Nonpolymer details | INHIBITOR 2-NITROBENZAMIDOMETHYLBORONIC ACID IS REPRESENTED BY TRIHYDROXY-[[(2-NITROPHENYL) ...INHIBITOR 2-NITROBENZA | |
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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: 2.58 Å3/Da / Density % sol: 52.01 % / 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: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1.0724 |
Detector | Type: MARRESEARCH SX-165 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0724 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→46 Å / Num. obs: 69063 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 99.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XDM Resolution: 2.5→42 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.9 / SU B: 23.2 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.598 / ESU R Free: 0.298 / 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: 39.546 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→42 Å
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Refine LS restraints |
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