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Yorodumi- PDB-3zg9: Crystal Structure of Penicillin-Binding Protein 4 from Listeria m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zg9 | ||||||
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Title | Crystal Structure of Penicillin-Binding Protein 4 from Listeria monocytogenes in the Cefuroxime bound form | ||||||
Components | (PENICILLIN-BINDING PROTEIN 4) x 2 | ||||||
Keywords | PENICILLIN-BINDING PROTEIN | ||||||
Function / homology | Function and homology information peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / response to antibiotic / proteolysis / membrane Similarity search - Function | ||||||
Biological species | LISTERIA MONOCYTOGENES (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.804 Å | ||||||
Authors | Jeong, J.H. / Kim, Y.G. | ||||||
Citation | Journal: To be Published Title: Crystal Structures of Penicillin-Binding Protein 4 from Listeria Monocytogenes Authors: Jeong, J.H. / Kim, Y.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zg9.cif.gz | 210.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zg9.ent.gz | 174 KB | Display | PDB format |
PDBx/mmJSON format | 3zg9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zg/3zg9 ftp://data.pdbj.org/pub/pdb/validation_reports/zg/3zg9 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 5049.557 Da / Num. of mol.: 1 / Fragment: RESIDUES 73-119 Source method: isolated from a genetically manipulated source Details: PROTEOLYSIS FROM 120-177 / Source: (gene. exp.) LISTERIA MONOCYTOGENES (bacteria) / Plasmid: PPROEXHTA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q8Y547 | ||
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#2: Protein | Mass: 58099.547 Da / Num. of mol.: 1 / Fragment: RESIDUES 178-714 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LISTERIA MONOCYTOGENES (bacteria) / Plasmid: PPROEXHTA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q8Y547 | ||
#3: Chemical | ChemComp-DXF / ( | ||
#4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.64 Å3/Da / Density % sol: 24.97 % / Description: NONE |
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Crystal grow | pH: 7 Details: 20% POLYETHYLENE GLYCOL 3350, 0.1M AMMONIUM TARTRATE (PH 7.0) |
-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.9795 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 25, 2010 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 47183 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 21.93 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 24 |
Reflection shell | Resolution: 1.8→1.87 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.1 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.804→29.795 Å / SU ML: 0.2 / σ(F): 1.49 / Phase error: 19.59 / 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: 1.804→29.795 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 4.5406 Å / Origin y: -21.738 Å / Origin z: -30.4566 Å
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Refinement TLS group | Selection details: ALL |