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Yorodumi- PDB-3beb: Crystal structure of E. coli penicillin-binding protein 5 in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3beb | ||||||
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Title | Crystal structure of E. coli penicillin-binding protein 5 in complex with a peptide-mimetic penicillin | ||||||
Components | Penicillin-binding protein 5 | ||||||
Keywords | HYDROLASE / PEPTIDOGLYCAN SYNTHESIS / PENICILLIN-BINDING PROTEIN / DD-CARBOXYPEPTIDASE / DESIGNED PENICILLIN / Cell shape / Cell wall biogenesis/degradation / Inner membrane / Membrane / Protease | ||||||
Function / homology | Function and homology information peptidoglycan metabolic process / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / carboxypeptidase activity / cell wall organization / beta-lactamase activity / beta-lactamase / regulation of cell shape ...peptidoglycan metabolic process / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / carboxypeptidase activity / cell wall organization / beta-lactamase activity / beta-lactamase / regulation of cell shape / outer membrane-bounded periplasmic space / protein homodimerization activity / proteolysis / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Heilemann, J. / Powell, A.J. / Davies, C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Crystal structures of complexes of bacterial DD-peptidases with peptidoglycan-mimetic ligands: the substrate specificity puzzle Authors: Sauvage, E. / Powell, A.J. / Heilemann, J. / Josephine, H.R. / Charlier, P. / Davies, C. / Pratt, R.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3beb.cif.gz | 87.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3beb.ent.gz | 64.4 KB | Display | PDB format |
PDBx/mmJSON format | 3beb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3beb_validation.pdf.gz | 838.5 KB | Display | wwPDB validaton report |
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Full document | 3beb_full_validation.pdf.gz | 841.7 KB | Display | |
Data in XML | 3beb_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 3beb_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/3beb ftp://data.pdbj.org/pub/pdb/validation_reports/be/3beb | HTTPS FTP |
-Related structure data
Related structure data | 2vgjC 2vgkC 3becC 1nzoS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39841.117 Da / Num. of mol.: 1 / Fragment: sequence database residues 30-386 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dacA, pfv / Plasmid: PBR322 / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061 References: UniProt: P0AEB2, serine-type D-Ala-D-Ala carboxypeptidase, beta-lactamase |
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#2: Chemical | ChemComp-HJ3 / ( |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Sequence details | THE AUTHORS' STATE THAT THIS IS A SOLUBLE CONSTRUCT OF A MUTANT PBP 5, TERMED SPBP 5 TO PRODUCE ...THE AUTHORS' STATE THAT THIS IS A SOLUBLE CONSTRUCT OF A MUTANT PBP 5, TERMED SPBP 5 TO PRODUCE SPBP 5, THE LAST 17 AMINO ACIDS WERE REMOVED BY DELETION OF THEIR RESPECTIVE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.05 % |
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Crystal grow | Temperature: 294 K / pH: 8 Details: 100mM Tris pH 8.0, 8% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 294K, pH 8.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 23, 2004 / Details: MIRRORS |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→47 Å / Num. obs: 25433 / % possible obs: 94.3 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 2 / % possible all: 85.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1NZO Resolution: 2→47 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.871 / SU B: 6.149 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.239 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 28.01 Å2
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Refinement step | Cycle: LAST / Resolution: 2→47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 Å / Total num. of bins used: 20
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