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- PDB-2v2f: Crystal structure of PBP1a from drug-resistant strain 5204 from S... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2v2f | ||||||
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Title | Crystal structure of PBP1a from drug-resistant strain 5204 from Streptococcus pneumoniae | ||||||
![]() | (PENICILLIN BINDING PROTEIN 1A) x 2 | ||||||
![]() | TRANSFERASE / TRANSPEPTIDASE ACTIVITY / PEPTIDOGLYCAN SYNTHESIS / HYDROLASE | ||||||
Function / homology | ![]() peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / membrane => GO:0016020 Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Job, V. / Carapito, R. / Vernet, T. / Dideberg, O. / Dessen, A. / Zapun, A. | ||||||
![]() | ![]() Title: Common Alterations in Pbp1A from Resistant Streptococcus Pneumoniae Decrease its Reactivity Toward {Beta}-Lactams: Structural Insights. Authors: Job, V. / Carapito, R. / Vernet, T. / Dessen, A. / Zapun, 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 | ![]() | 94.1 KB | Display | ![]() |
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PDB format | ![]() | 68.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2cw6S 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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Unit cell |
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Components
#1: Protein/peptide | Mass: 2639.935 Da / Num. of mol.: 1 / Fragment: GLYCOSYLTRASFERASE DOMAIN, RESIDUES 47-70 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9RET4, peptidoglycan glycosyltransferase |
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#2: Protein | Mass: 43432.023 Da / Num. of mol.: 1 Fragment: TRANSPEPTIDASE DOMAIN, GLYCOSYLTRASFERASE DOMAIN, RESIDUES 264-653 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9RET4, serine-type D-Ala-D-Ala carboxypeptidase |
#3: Chemical | ChemComp-BA / |
#4: Chemical | ChemComp-MES / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 45.9 % / Description: NONE |
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Crystal grow | pH: 6 / Details: 0.1M MES PH6, 21% PEG6000, 17MM BACL2 |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 5, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→19.7 Å / Num. obs: 29802 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 3.77 % / Biso Wilson estimate: 18.23 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.9→2.06 Å / Redundancy: 3.86 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4 / % possible all: 93.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2CW6 Resolution: 1.9→19.74 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.876 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.166 / 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: 13.11 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→19.74 Å
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Refine LS restraints |
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