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- PDB-1rp5: PBP2x from Streptococcus pneumoniae strain 5259 with reduced susc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1rp5 | ||||||
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Title | PBP2x from Streptococcus pneumoniae strain 5259 with reduced susceptibility to beta-lactam antibiotics | ||||||
![]() | penicillin-binding protein 2x | ||||||
![]() | TRANSPEPTIDASE / PENICILLIN-BINDING PROTEIN / ANTIBIOTIC RESISTANCE / PEPTIDOGLYCAN SYNTHESIS / CELL WALL / TRANSMEMBRANE | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pernot, L. / Chesnel, L. / Legouellec, A. / Croize, J. / Vernet, T. / Dideberg, O. / Dessen, A. | ||||||
![]() | ![]() Title: A PBP2x from a clinical isolate of Streptococcus pneumoniae exhibits an alternative mechanism for reduction of susceptibility to beta-lactam antibiotics. Authors: Pernot, L. / Chesnel, L. / Le Gouellec, A. / Croize, J. / Vernet, T. / Dideberg, O. / Dessen, A. #1: ![]() Title: The Structural Modifications Induced by the M339F Substitution in PBP2x from Streptococcus pneumoniae Further Decreases the Susceptibility to Beta-Lactams of Resistant Strains Authors: Chesnel, L. / Pernot, L. / Lemaire, D. / Champelovier, D. / Croize, J. / Dideberg, O. / Vernet, T. / Zapun, A. #2: ![]() Title: Crystal structure of pbp2x from a highly penicillin-resistant streptococcus pneumoniae clinical isolate Authors: Dessen, A. / Mouz, N. / Gordon, E. / Hopkins, J. / Dideberg, O. #3: ![]() Title: The crystal structure of the penicillin-binding protein 2x from Streptococcus pneumoniae and its acyl-enzyme form: implication in drug resistance Authors: Gordon, E. / Mouz, N. / Duee, E. / Dideberg, O. #4: ![]() Title: X-ray structure of Streptococcus pneumoniae PBP2x, a primary penicillin target enzyme Authors: Pares, S. / Mouz, N. / Petillot, Y. / Hakenbeck, R. / Dideberg, O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 263.5 KB | Display | ![]() |
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PDB format | ![]() | 211.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.7 KB | Display | ![]() |
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Full document | ![]() | 488.3 KB | Display | |
Data in XML | ![]() | 50.5 KB | Display | |
Data in CIF | ![]() | 68.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qmeS S: Starting model for refinement |
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Similar structure data |
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Links
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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 | Mass: 76906.031 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P14677, Hydrolases; Acting on peptide bonds (peptidases) #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.76 Å3/Da / Density % sol: 74 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 4.3 Details: PEG 1500, SODIUM ACETATE, AMMONIUM SULFATE, pH 4.3, VAPOR DIFFUSION, HANGING DROP, temperature 281K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 8 ℃ / pH: 8 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 17, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97936 Å / Relative weight: 1 |
Reflection | Resolution: 3→42 Å / Num. obs: 57788 / % possible obs: 96.5 % / Observed criterion σ(I): 2 / Redundancy: 11.4 % / Rsym value: 0.092 / Net I/σ(I): 29.7 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 3 / Rsym value: 0.426 / % possible all: 77.2 |
Reflection | *PLUS Num. measured all: 657234 / Rmerge(I) obs: 0.092 |
Reflection shell | *PLUS % possible obs: 77.2 % / Rmerge(I) obs: 0.426 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QME Resolution: 3→42 Å / Rfactor Rfree error: 0.004 / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 59.1 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Refinement | *PLUS Lowest resolution: 42 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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