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Yorodumi- PDB-5oj1: Penicillin Binding Protein 2x (PBP2x) from S.pneumoniae in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oj1 | ||||||
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Title | Penicillin Binding Protein 2x (PBP2x) from S.pneumoniae in complex with Oxacillin and a tetrasaccharide | ||||||
Components | Penicillin-binding protein 2X | ||||||
Keywords | ANTIBIOTIC / Penicillin-binding-protein / cell-wall | ||||||
Function / homology | Function and homology information penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / response to antibiotic / plasma membrane Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae R6 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Bernardo-Garcia, N. / Hermoso, J.A. | ||||||
Citation | Journal: ACS Chem. Biol. / Year: 2018 Title: Allostery, Recognition of Nascent Peptidoglycan, and Cross-linking of the Cell Wall by the Essential Penicillin-Binding Protein 2x of Streptococcus pneumoniae. Authors: Bernardo-Garcia, N. / Mahasenan, K.V. / Batuecas, M.T. / Lee, M. / Hesek, D. / Petrackova, D. / Doubravova, L. / Branny, P. / Mobashery, S. / Hermoso, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oj1.cif.gz | 146.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oj1.ent.gz | 113.1 KB | Display | PDB format |
PDBx/mmJSON format | 5oj1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/5oj1 ftp://data.pdbj.org/pub/pdb/validation_reports/oj/5oj1 | HTTPS FTP |
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-Related structure data
Related structure data | 5oauC 5oizC 5oj0C 1k25S 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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Unit cell |
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-Components
#1: Protein | Mass: 76807.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae R6 (bacteria) / Gene: pbpX, spr0304 / Production host: Escherichia coli (E. coli) / References: UniProt: P59676 |
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#2: Chemical | ChemComp-1S6 / ( |
#3: Chemical | ChemComp-NA / |
#4: 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: 3.75 Å3/Da / Density % sol: 67.24 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 2.3-3M NaCl, 0.1M Na Acetate pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97497 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97497 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→48.72 Å / Num. obs: 26783 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.078 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.85→3 Å / Redundancy: 7 % / Rmerge(I) obs: 1.7 / Mean I/σ(I) obs: 1.3 / Rpim(I) all: 0.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1K25 Resolution: 2.85→87.33 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.897 / SU B: 8.155 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.532 / ESU R Free: 0.302 / 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: 70.969 Å2
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Refinement step | Cycle: 1 / Resolution: 2.85→87.33 Å
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Refine LS restraints |
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