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Yorodumi- PDB-2y2p: Penicillin-binding protein 1b (pbp-1b) in complex with an alkyl b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y2p | ||||||
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Title | Penicillin-binding protein 1b (pbp-1b) in complex with an alkyl boronate (z10) | ||||||
Components | PENICILLIN-BINDING PROTEIN 1B | ||||||
Keywords | TRANSFERASE / CELL WALL / PEPTIDOGLYCAN / INHIBITOR | ||||||
Function / homology | Function and homology information peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / penicillin binding / peptidoglycan biosynthetic process / response to antibiotic / proteolysis / extracellular region ...peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / penicillin binding / peptidoglycan biosynthetic process / response to antibiotic / proteolysis / extracellular region / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | STREPTOCOCCUS PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | ||||||
Authors | 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. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y2p.cif.gz | 201.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y2p.ent.gz | 160.2 KB | Display | PDB format |
PDBx/mmJSON format | 2y2p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y2/2y2p ftp://data.pdbj.org/pub/pdb/validation_reports/y2/2y2p | HTTPS FTP |
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-Related structure data
Related structure data | 2y2gC 2y2hC 2y2iC 2y2jC 2y2kC 2y2lC 2y2mC 2y2nC 2y2oC 2y2qC 2bg1S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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
#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 (Z10) COVALENTLY BOND TO S460 / Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: R6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYS References: UniProt: Q7CRA4, peptidoglycan glycosyltransferase, Transferases; Acyltransferases; Aminoacyltransferases | ||||||||
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#2: Chemical | ChemComp-Z10 / [( | ||||||||
#3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, ASN 656 TO GLY ENGINEERED RESIDUE IN CHAIN A, ARG 686 TO GLN ...ENGINEERED | Nonpolymer details | (S)-(1-(3-FLUORO-[1, 1'-BIPHENYL]-2-YLCARBOXAM | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.55 % Description: MOLECULAR REPLACEMENT MODEL 2BG1 WITHOUT RESIDUES 654 TO 660 |
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Crystal grow | pH: 7.2 Details: 50MM HEPES PH 7.2, 3M NACL, 0.6-0.9M AMMONIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 19, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→44.4 Å / Num. obs: 89431 / % possible obs: 79.7 % / Observed criterion σ(I): 3 / Redundancy: 5.1 % / Biso Wilson estimate: 32.275 Å2 / Rsym value: 0.04 / Net I/σ(I): 35.58 |
Reflection shell | Resolution: 1.62→1.72 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.47 / % possible all: 52.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BG1 Resolution: 1.62→44.39 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 6.168 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.1 / 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: 34.641 Å2
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Refinement step | Cycle: LAST / Resolution: 1.62→44.39 Å
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Refine LS restraints |
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