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Yorodumi- PDB-2uwx: Active site restructuring regulates ligand recognition in class A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2uwx | |||||||||
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Title | Active site restructuring regulates ligand recognition in class A penicillin-binding proteins | |||||||||
Components | PENICILLIN-BINDING PROTEIN 1B | |||||||||
Keywords | TRANSFERASE / PEPTIDOGLYCAN SYNTHESIS MULTIFUNCTIONAL ENZYME / ACYLTRANSFERASE / GLYCOSYLTRANSFERASE / CELL WALL / PEPTIDOGLYCAN | |||||||||
Function / homology | Function and homology information peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / penicillin binding / peptidoglycan biosynthetic process / response to antibiotic / proteolysis / extracellular region ...peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / penicillin binding / peptidoglycan biosynthetic process / response to antibiotic / proteolysis / extracellular region / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | STREPTOCOCCUS PNEUMONIAE (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å | |||||||||
Authors | Macheboeuf, P. / DiGuilmi, A.M. / Job, V. / Vernet, T. / Dideberg, O. / Dessen, A. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2005 Title: Active Site Restructuring Regulates Ligand Recognition in Class a Penicillin-Binding Proteins Authors: Macheboeuf, P. / Di Guilmi, A.M. / Job, V. / Vernet, T. / Dideberg, O. / Dessen, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2uwx.cif.gz | 112.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2uwx.ent.gz | 85.3 KB | Display | PDB format |
PDBx/mmJSON format | 2uwx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2uwx_validation.pdf.gz | 453.6 KB | Display | wwPDB validaton report |
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Full document | 2uwx_full_validation.pdf.gz | 461.3 KB | Display | |
Data in XML | 2uwx_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 2uwx_validation.cif.gz | 33.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/2uwx ftp://data.pdbj.org/pub/pdb/validation_reports/uw/2uwx | HTTPS FTP |
-Related structure data
Related structure data | 2bg1SC 2xd1C 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 54657.414 Da / Num. of mol.: 1 / Fragment: RESIDUES 101-125,323-791 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: R6 / Plasmid: PGEX4T1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q7CRA4, peptidoglycan glycosyltransferase, Transferases; Acyltransferases; Aminoacyltransferases | ||||||
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#2: Chemical | ChemComp-SO4 / | ||||||
#3: Chemical | #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61 % |
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Crystal grow | pH: 7 Details: 50 MM HEPES PH7 0.8 M AMMONIUM SULFATE 2.8 M SODIUM CHLORIDE, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 25660 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 25.6 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.8 / % possible all: 99 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BG1 Resolution: 2.39→81.65 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.588 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.213 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.39→81.65 Å
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