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Yorodumi- PDB-3zvw: Unexpected tricovalent binding mode of boronic acids within the a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zvw | |||||||||
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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 / PEPTIDOGLYCAN / PENICILLIN-BINDING / TETRAVALENT BORON | |||||||||
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 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 | 3zvw.cif.gz | 737.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zvw.ent.gz | 617 KB | Display | PDB format |
PDBx/mmJSON format | 3zvw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/3zvw ftp://data.pdbj.org/pub/pdb/validation_reports/zv/3zvw | HTTPS FTP |
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-Related structure data
Related structure data | 2y4aC 2y55C 2y59C 3zvtC 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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1 |
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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
-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 , 7 types, 1993 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-MES / | #8: 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: 2.34 Å3/Da / Density % sol: 46.91 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9798 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 2→34.73 Å / Num. obs: 134070 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.5 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XDM Resolution: 2→34.59 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.92 / SU B: 9.016 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.162 / 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: 28.158 Å2
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Refinement step | Cycle: LAST / Resolution: 2→34.59 Å
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Refine LS restraints |
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