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Yorodumi- PDB-2z2m: Cefditoren-Acylated Penicillin-Binding Protein 2X (PBP2X) from St... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z2m | ||||||
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Title | Cefditoren-Acylated Penicillin-Binding Protein 2X (PBP2X) from Streptococcus pneumoniae | ||||||
Components | (Penicillin-binding protein ...) x 3 | ||||||
Keywords | BIOSYNTHETIC PROTEIN / PEPTIDOGLYCAN SYNTHESIS / CELL WALL / PENICILLIN-BINDING / ANTIBIOTICS / CEFDITOREN | ||||||
Function / homology | Function and homology information penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / response to antibiotic / plasma membrane Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Yamada, M. / Watanabe, T. / Takeuchi, Y. | ||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2007 Title: Crystal Structure of Cefditoren Complexed with Streptococcus pneumoniae Penicillin-Binding Protein 2X: Structural Basis for its High Antimicrobial Activity Authors: Yamada, M. / Watanabe, T. / Miyara, T. / Baba, N. / Saito, J. / Takeuchi, Y. / Ohsawa, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z2m.cif.gz | 243.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z2m.ent.gz | 194.9 KB | Display | PDB format |
PDBx/mmJSON format | 2z2m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z2/2z2m ftp://data.pdbj.org/pub/pdb/validation_reports/z2/2z2m | HTTPS FTP |
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-Related structure data
Related structure data | 2z2lSC 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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Unit cell |
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-Components
-Penicillin-binding protein ... , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 18473.584 Da / Num. of mol.: 2 / Fragment: UNP residues 71-238 Source method: isolated from a genetically manipulated source Details: N-TERMINAL DOMAIN / Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: pbpX / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: P59676, UniProt: P14677*PLUS #2: Protein | Mass: 42000.016 Da / Num. of mol.: 2 / Fragment: UNP residues 241-625 Source method: isolated from a genetically manipulated source Details: TRANSPEPTIDASE DOMAIN / Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: pbpX / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: P59676, UniProt: P14677*PLUS #3: Protein | Mass: 13707.433 Da / Num. of mol.: 2 / Fragment: UNP residues 626-750 Source method: isolated from a genetically manipulated source Details: C-TERMINAL DOMAIN / Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: pbpX / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: P59676, UniProt: P14677*PLUS |
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-Non-polymers , 3 types, 96 molecules
#4: Chemical | ChemComp-SO4 / | ||
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#5: Chemical | #6: Water | ChemComp-HOH / | |
-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: 55.59 % |
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Crystal grow | Method: vapor diffusion, hanging drop Details: 10-25% PEG4000, 0.2M ammonium sulfate, 0.1M sodium acetate, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32B2 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 11, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 46229 / % possible obs: 89.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 60.179 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 4 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 5.5 / % possible all: 90.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Z2L Resolution: 2.6→29.42 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.898 / SU B: 10.142 / SU ML: 0.22 / Cross valid method: THROUGHOUT / ESU R: 0.805 / ESU R Free: 0.343 / 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: 46.402 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→29.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.667 Å / Total num. of bins used: 20
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