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- PDB-5df7: CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 3 FROM PSEUDOMONA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5df7 | ||||||
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Title | CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 3 FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH AZLOCILLIN | ||||||
![]() | Cell division protein | ||||||
![]() | TRANSFERASE / azlocillin / beta-lactam antibiotics / acyl-enzyme complex / de-acylation | ||||||
Function / homology | ![]() peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / proteolysis / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ren, J. / Nettleship, J.E. / Males, A. / Stuart, D.I. / Owens, R.J. | ||||||
![]() | ![]() Title: Crystal structures of penicillin-binding protein 3 in complexes with azlocillin and cefoperazone in both acylated and deacylated forms. Authors: Ren, J. / Nettleship, J.E. / Males, A. / Stuart, D.I. / Owens, R.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 400.3 KB | Display | ![]() |
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PDB format | ![]() | 322.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5df8C ![]() 5df9C ![]() 4kqoS 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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 61152.590 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: pbpB, ftsI_2, ERS445055_04698, PAE221_03076, YQ19_27590 Production host: ![]() ![]() References: UniProt: Q51504, peptidoglycan glycosyltransferase |
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-Non-polymers , 5 types, 393 molecules ![](data/chem/img/59H.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.05 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 2.5 M NaCl; 0.1 M imidazole pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 30, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 76005 / % possible obs: 86.7 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 1.6 / % possible all: 78.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4KQO Resolution: 2→47.19 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 9.276 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.265 Å2
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Refinement step | Cycle: 1 / Resolution: 2→47.19 Å
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Refine LS restraints |
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