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Yorodumi- PDB-3zg8: Crystal Structure of Penicillin Binding Protein 4 from Listeria m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zg8 | ||||||
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Title | Crystal Structure of Penicillin Binding Protein 4 from Listeria monocytogenes in the Ampicillin bound form | ||||||
Components |
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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: 2.094 Å | ||||||
Authors | Jeong, J.H. / Kim, Y.G. | ||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2013 Title: Crystal Structures of Bifunctional Penicillin-Binding Protein 4 from Listeria Monocytogenes. Authors: Jeong, J. / Kim, Y. / Rojviriya, C. / Ha, S. / Kang, B.S. / Kim, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zg8.cif.gz | 114.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zg8.ent.gz | 85.1 KB | Display | PDB format |
PDBx/mmJSON format | 3zg8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zg8_validation.pdf.gz | 893.8 KB | Display | wwPDB validaton report |
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Full document | 3zg8_full_validation.pdf.gz | 901.4 KB | Display | |
Data in XML | 3zg8_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 3zg8_validation.cif.gz | 29.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zg/3zg8 ftp://data.pdbj.org/pub/pdb/validation_reports/zg/3zg8 | HTTPS FTP |
-Related structure data
Related structure data | 3zg7SC 3zgaC S: Starting model for refinement C: citing same article (ref.) |
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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
#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-AIX / ( | ||
#4: Chemical | #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: 1.91 Å3/Da / Density % sol: 35.75 % / Description: NONE |
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Crystal grow | pH: 7 Details: 20% POLYETHYLENE GLYCOL 3,350 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 20, 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: 2.1→30 Å / Num. obs: 35362 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 32.48 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 27.3 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.5 / % possible all: 88.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZG7 Resolution: 2.094→29.698 Å / SU ML: 0.27 / σ(F): 1.48 / Phase error: 22.87 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.094→29.698 Å
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Refine LS restraints |
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LS refinement shell |
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