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- PDB-2y2j: 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: 2y2j | ||||||
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Title | PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (ZA4) | ||||||
![]() | PENICILLIN-BINDING PROTEIN 1B | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Contreras-Martel, C. / Amoroso, A. / Woon, E.C. / Zervosen, A. / Inglis, S. / Martins, A. / Verlaine, O. / Rydzik, A. / Job, V. / Luxen, A. ...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. | ||||||
![]() | ![]() 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 | ![]() | 205 KB | Display | ![]() |
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PDB format | ![]() | 163.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2y2gC ![]() 2y2hC ![]() 2y2iC ![]() 2y2kC ![]() 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 (ZA4) COVALENTLY BOND TO S460 / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: Q7CRA4, ![]() ![]() |
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-Non-polymers , 6 types, 294 molecules ![](data/chem/img/ZA4.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-ZA4 / [( | ||||||
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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-FLUOROBENZ |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.01 % 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![]() |
Reflection | Resolution: 2.06→49 Å / Num. obs: 43115 / % possible obs: 90.3 % / Observed criterion σ(I): 3 / Redundancy: 6.3 % / Biso Wilson estimate: 42.269 Å2 / Rsym value: 0.05 / Net I/σ(I): 31.8 |
Reflection shell | Resolution: 2.06→2.19 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.45 / % possible all: 71.1 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2BG1 Resolution: 2.06→48.98 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.875 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.152 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.257 Å2
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Refinement step | Cycle: LAST / Resolution: 2.06→48.98 Å
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Refine LS restraints |
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