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- PDB-6hzo: Apo structure of TP domain from Haemophilus influenzae Penicillin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6hzo | ||||||
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Title | Apo structure of TP domain from Haemophilus influenzae Penicillin-Binding Protein 3 | ||||||
![]() | FtsI | ||||||
![]() | PEPTIDE BINDING PROTEIN / penicillin-binding protein / peptidoglycan / Transpeptidase | ||||||
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 / plasma membrane => GO:0005886 / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bellini, D. / Koekemoer, L. / Newman, H. / Dowson, C.G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Novel and Improved Crystal Structures of H. influenzae, E. coli and P. aeruginosa Penicillin-Binding Protein 3 (PBP3) and N. gonorrhoeae PBP2: Toward a Better Understanding of beta-Lactam ...Title: Novel and Improved Crystal Structures of H. influenzae, E. coli and P. aeruginosa Penicillin-Binding Protein 3 (PBP3) and N. gonorrhoeae PBP2: Toward a Better Understanding of beta-Lactam Target-Mediated Resistance. Authors: Bellini, D. / Koekemoer, L. / Newman, H. / Dowson, C.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 222.9 KB | Display | ![]() |
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PDB format | ![]() | 179.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6hzjC ![]() 6hzqC ![]() 6hzrC ![]() 6i1eC ![]() 6i1iC ![]() 6r3xC ![]() 6r40C ![]() 6r42C ![]() 4bjpS 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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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35350.430 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.77 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3,350 and 0.2 M KNO3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.44→95.4 Å / Num. obs: 33806 / % possible obs: 91.8 % / Redundancy: 4.4 % / Rrim(I) all: 0.086 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.44→2.69 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4BJP Resolution: 2.44→95.4 Å / Cor.coef. Fo:Fc: 0.93 / SU B: 12.234 / SU ML: 0.254 / Cross valid method: FREE R-VALUE / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.372 Å2
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Refinement step | Cycle: 1 / Resolution: 2.44→95.4 Å
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Refine LS restraints |
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