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- PDB-5oiz: Penicillin-Binding Protein 2X (PBP2X) from Streptococcus pneumoni... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5oiz | ||||||
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Title | Penicillin-Binding Protein 2X (PBP2X) from Streptococcus pneumoniae in complex with oxacillin | ||||||
![]() | Penicillin-binding protein 2X | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bernardo-Garcia, N. / Hermoso, J.A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 260.4 KB | Display | ![]() |
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PDB format | ![]() | 208 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5oauC ![]() 5oj0C ![]() 5oj1C ![]() 1k25S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() Gene: pbpX, spr0304 / Production host: ![]() ![]() ![]() |
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#2: Chemical | ChemComp-1S6 / (![]() |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.56 Å3/Da / Density % sol: 65.45 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 2.3-3.0 M NaCl, 0.1 M sodium acetate pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.7→86.79 Å / Num. obs: 30875 / % possible obs: 99.7 % / Redundancy: 3.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.078 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.7→2.83 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.14 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4451 / CC1/2: 0.58 / Rpim(I) all: 0.67 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1K25 Resolution: 2.7→48.54 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.908 / SU B: 10.963 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.068 / 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: 63.405 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→48.54 Å
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Refine LS restraints |
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