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Yorodumi- PDB-4cjn: Crystal structure of PBP2a from MRSA in complex with quinazolinon... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cjn | ||||||
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Title | Crystal structure of PBP2a from MRSA in complex with quinazolinone ligand | ||||||
Components | PENICILLIN BINDING PROTEIN 2 PRIME | ||||||
Keywords | HYDROLASE / IMMUNE SYSTEM / ALLOSTERIC SITE | ||||||
Function / homology | Function and homology information serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / membrane => GO:0016020 / response to antibiotic / membrane Similarity search - Function | ||||||
Biological species | STAPHYLOCOCCUS AUREUS SUBSP. AUREUS MU50 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.947 Å | ||||||
Authors | Bouley, R. / Otero, L.H. / Rojas-Altuve, A. / Hermoso, J.A. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2015 Title: Discovery of Antibiotic (E)-3-(3-Carboxyphenyl)-2-(4-Cyanostyryl)Quinazolin-4(3H)-One. Authors: Bouley, R. / Kumarasiri, M. / Peng, Z. / Otero, L.H. / Song, W. / Suckow, M.A. / Schroeder, V.A. / Wolter, W.R. / Lastochkin, E. / Antunes, N.T. / Pi, H. / Vakulenko, S. / Hermoso, J.A. / ...Authors: Bouley, R. / Kumarasiri, M. / Peng, Z. / Otero, L.H. / Song, W. / Suckow, M.A. / Schroeder, V.A. / Wolter, W.R. / Lastochkin, E. / Antunes, N.T. / Pi, H. / Vakulenko, S. / Hermoso, J.A. / Chang, M. / Mobashery, S. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: How Allosteric Control of Staphylococcus Aureus Penicillin Binding Protein 2A Enables Methicillin Resistance and Physiological Function. Authors: Otero, L.H. / Rojas-Altuve, A. / Llarrull, L.I. / Carrasco-Lopez, C. / Kumarasiri, M. / Lastochkin, E. / Fishovitz, J. / Dawley, M. / Hesek, D. / Lee, M. / Johnson, J.W. / Fisher, J.F. / ...Authors: Otero, L.H. / Rojas-Altuve, A. / Llarrull, L.I. / Carrasco-Lopez, C. / Kumarasiri, M. / Lastochkin, E. / Fishovitz, J. / Dawley, M. / Hesek, D. / Lee, M. / Johnson, J.W. / Fisher, J.F. / Chang, M. / Mobashery, S. / Hermoso, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cjn.cif.gz | 539.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cjn.ent.gz | 443.3 KB | Display | PDB format |
PDBx/mmJSON format | 4cjn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cjn_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 4cjn_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 4cjn_validation.xml.gz | 48.6 KB | Display | |
Data in CIF | 4cjn_validation.cif.gz | 67.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cj/4cjn ftp://data.pdbj.org/pub/pdb/validation_reports/cj/4cjn | HTTPS FTP |
-Related structure data
Related structure data | 3zg0S 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
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 73286.656 Da / Num. of mol.: 2 / Fragment: RESIDUES 27-668 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STAPHYLOCOCCUS AUREUS SUBSP. AUREUS MU50 (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR References: UniProt: Q54113, UniProt: A0A0J9X1X5*PLUS, serine-type D-Ala-D-Ala carboxypeptidase #4: Sugar | |
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-Non-polymers , 4 types, 304 molecules
#2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-CL / #5: Chemical | ChemComp-QNZ / ( | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 54.01 % / Description: NONE |
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Crystal grow | pH: 7 / Details: PH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→63.96 Å / Num. obs: 115623 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 25.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 18.4 % / Mean I/σ(I) obs: 1.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZG0 Resolution: 1.947→63.876 Å / SU ML: 0.26 / σ(F): 1.33 / Phase error: 33.51 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.947→63.876 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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