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- PDB-2y2k: PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL B... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2y2k | ||||||
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Title | PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (ZA5) | ||||||
![]() | PENICILLIN-BINDING PROTEIN 1B | ||||||
![]() | TRANSFERASE / INFECTION / CELL WALL / PEPTIDOGLYCAN / INHIBITOR | ||||||
Function / homology | ![]() peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase activity / acyltransferase activity / penicillin binding / peptidoglycan biosynthetic process / response to antibiotic / proteolysis / extracellular region / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Contreras-Martel, C. / Amoroso, A. / Woon, E. / Zervosen, A. / Inglis, S. / Martins, A. / Verlaine, O. / Rydzik, A. / Job, V. / Luxen, A. ...Contreras-Martel, C. / Amoroso, A. / Woon, E. / Zervosen, A. / Inglis, S. / Martins, A. / Verlaine, O. / Rydzik, A. / Job, V. / Luxen, A. / Joris, B. / Schofield, C. / Dessen, A. | ||||||
![]() | ![]() Title: Structure-Guided Design of Cell Wall Biosynthesis Inhibitors that Overcome Beta-Lactam Resistance in Staphylococcus Aureus (Mrsa). Authors: Contreras-Martel, C. / Amoroso, A. / Woon, E.C. / Zervosen, A. / Inglis, S. / Martins, A. / Verlaine, O. / Rydzik, A. / Job, V. / Luxen, A. / Joris, B. / Schofield, C.J. / Dessen, 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 | ![]() | 204.4 KB | Display | ![]() |
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PDB format | ![]() | 162 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 466.4 KB | Display | ![]() |
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Full document | ![]() | 475.4 KB | Display | |
Data in XML | ![]() | 21.8 KB | Display | |
Data in CIF | ![]() | 31.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2y2gC ![]() 2y2hC ![]() 2y2iC ![]() 2y2jC ![]() 2y2lC ![]() 2y2mC ![]() 2y2nC ![]() 2y2oC ![]() 2y2pC ![]() 2y2qC ![]() 2bg1S C: citing same article ( 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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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 54096.906 Da / Num. of mol.: 1 / Fragment: TRANSPEPTIDASE DOMAIN, RESIDUES 101-125,323-791 / Mutation: YES Source method: isolated from a genetically manipulated source Details: ALKYL BORONATE (ZA5) COVALENTLY BOND TO S460 / Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q7CRA4, peptidoglycan glycosyltransferase, Transferases; Acyltransferases; Aminoacyltransferases |
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-Non-polymers , 6 types, 230 molecules ![](data/chem/img/ZA5.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZA5 / [( | ||||||
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#3: Chemical | ChemComp-SO4 / | ||||||
#4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-NA / | #6: Chemical | ChemComp-EDO / | #7: Water | ChemComp-HOH / | |
-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, ASN 656 TO GLY ENGINEERED RESIDUE IN CHAIN A, ARG 686 TO GLN ...ENGINEERED |
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Nonpolymer details | ((2,6-DIFLUOROBE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.47 % Description: MOLECULAR REPLACEMENT MODEL 2BG1 WITHOUT RESIDUES 654 TO 660 |
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Crystal grow | pH: 7.2 Details: 50 MM HEPES PH 7.2, 3M NACL, 0.6-0.9 M AMMONIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 3, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→44.5 Å / Num. obs: 41196 / % possible obs: 82.8 % / Observed criterion σ(I): 3 / Redundancy: 5.1 % / Biso Wilson estimate: 42.727 Å2 / Rsym value: 0.06 / Net I/σ(I): 30.4 |
Reflection shell | Resolution: 2.09→2.22 Å / Redundancy: 5 % / Mean I/σ(I) obs: 3.56 / Rsym value: 0.5 / % possible all: 58.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2BG1 Resolution: 2.09→44.55 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.926 / SU B: 8.987 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED.
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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: 47.54 Å2
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Refinement step | Cycle: LAST / Resolution: 2.09→44.55 Å
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Refine LS restraints |
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