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Yorodumi- PDB-2zc6: Penicillin-binding protein 1A (PBP 1A) acyl-enzyme complex (tebip... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zc6 | ||||||
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Title | Penicillin-binding protein 1A (PBP 1A) acyl-enzyme complex (tebipenem) from Streptococcus pneumoniae | ||||||
Components | (Penicillin-binding protein 1A) x 2 | ||||||
Keywords | BIOSYNTHETIC PROTEIN / PEPTIDOGLYCAN SYNTHESIS / CELL WALL / PENICILLIN-BINDING / ANTIBIOTICS / TEBIPENEM / Antibiotic resistance / Cell shape / Cell wall biogenesis/degradation / Multifunctional enzyme / Secreted | ||||||
Function / homology | Function and homology information peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic / proteolysis ...peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic / proteolysis / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Yamada, M. / Watanabe, T. / Takeuchi, Y. | ||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2008 Title: Crystal Structures of Biapenem and Tebipenem Complexed with Penicillin-Binding Proteins 2X and 1A from Streptococcus pneumoniae Authors: Yamada, M. / Watanabe, T. / Baba, N. / Takeuchi, Y. / Ohsawa, F. / Gomi, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zc6.cif.gz | 167.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zc6.ent.gz | 131.9 KB | Display | PDB format |
PDBx/mmJSON format | 2zc6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/2zc6 ftp://data.pdbj.org/pub/pdb/validation_reports/zc/2zc6 | HTTPS FTP |
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-Related structure data
Related structure data | 2zc3C 2zc4C 2zc5C 2c6wS 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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2 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 2639.935 Da / Num. of mol.: 2 / Fragment: UNP residues 47-70 Source method: isolated from a genetically manipulated source Details: Transglycosylase domain / Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: pbpA, exp2 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DR59, UniProt: Q04707*PLUS #2: Protein | Mass: 43565.953 Da / Num. of mol.: 2 / Fragment: UNP residues 264-653 / Mutation: R545Q Source method: isolated from a genetically manipulated source Details: Transpeptidase domain / Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: pbp1a / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q549Y6, UniProt: Q04707*PLUS #3: Chemical | ChemComp-ZN / #4: Chemical | #5: 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: 2.77 Å3/Da / Density % sol: 55.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 0.004-0.006M ZINC SULFATE, 0.05M MES, pH6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2006 Details: Rotated-inclined double-crystal monochromator, rhodium-coated horizontal mirror |
Radiation | Monochromator: rotated-inclined double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→29.88 Å / Num. obs: 29074 / % possible obs: 100 % / Redundancy: 4.5 % / Biso Wilson estimate: 56.87 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 2.7 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2C6W Resolution: 2.7→29.88 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.873 / Cross valid method: THROUGHOUT / ESU R: 1.129 / ESU R Free: 0.359 / 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: 41.98 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→29.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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