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Yorodumi- PDB-2y55: Unexpected tricovalent binding mode of boronic acids within the a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y55 | ||||||
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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 CARBOXYPEPTIDASEMuramoylpentapeptide 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: 2.6 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 | 2y55.cif.gz | 682 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y55.ent.gz | 571.7 KB | Display | PDB format |
PDBx/mmJSON format | 2y55.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y5/2y55 ftp://data.pdbj.org/pub/pdb/validation_reports/y5/2y55 | HTTPS FTP |
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-Related structure data
Related structure data | 2y4aC 2y59C 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
-Protein , 1 types, 4 molecules ABCD
#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 |
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-Non-polymers , 5 types, 277 molecules
#2: Chemical | ChemComp-FP5 / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-ACN / #6: 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: 2.66 Å3/Da / Density % sol: 53.4 % / 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: 0.9797 |
Detector | Type: MARRESEARCH SX-165 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→41.3 Å / Num. obs: 57773 / % possible obs: 92.7 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 3 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.7 / % possible all: 83.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XDM Resolution: 2.6→38.9 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.902 / SU B: 29.445 / SU ML: 0.286 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.357 / 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: 64.5 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→38.9 Å
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