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- PDB-3zga: Crystal Structure of Penicillin-Binding Protein 4 from Listeria m... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3zga | ||||||
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Title | Crystal Structure of Penicillin-Binding Protein 4 from Listeria monocytogenes in the Carbenicillin bound form | ||||||
![]() | (PENICILLIN-BINDING PROTEIN 4) x 2 | ||||||
![]() | PENICILLIN-BINDING PROTEIN | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jeong, J.H. / Kim, Y.G. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 212.8 KB | Display | ![]() |
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PDB format | ![]() | 168.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 874 KB | Display | ![]() |
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Full document | ![]() | 877.9 KB | Display | |
Data in XML | ![]() | 20.8 KB | Display | |
Data in CIF | ![]() | 29.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3zg7SC ![]() 3zg8C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() | ||
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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 Details: CARBENICILLIN BOUND TO SER394, PROTEOLYSIS FROM 120-177 Source: (gene. exp.) ![]() ![]() ![]() | ||
#3: Chemical | ChemComp-CB9 / ( | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() |
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→30 Å / Num. obs: 39480 / % possible obs: 97.2 % / Observed criterion σ(I): 24.9 / Redundancy: 4.8 % / Biso Wilson estimate: 30.31 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 2→2.08 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.1 / % possible all: 85.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3ZG7 Resolution: 2.005→26.726 Å / SU ML: 0.24 / σ(F): 1.5 / Phase error: 22.33 / 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: 45.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.005→26.726 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: 11.364 Å / Origin y: -22.0677 Å / Origin z: -11.0694 Å
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Refinement TLS group | Selection details: ALL |