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- PDB-6hzj: Apo structure of TP domain from clinical penicillin-resistant mut... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6hzj | ||||||
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Title | Apo structure of TP domain from clinical penicillin-resistant mutant Neisseria gonorrhoea strain 6140 Penicillin-Binding Protein 2 (PBP2) | ||||||
![]() | Probable peptidoglycan D,D-transpeptidase PenA | ||||||
![]() | HYDROLASE / penicillin-binding protein / 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 ...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 / response to antibiotic / proteolysis / plasma membrane 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 | ![]() | 142.6 KB | Display | ![]() |
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PDB format | ![]() | 110.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441 KB | Display | ![]() |
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Full document | ![]() | 445.4 KB | Display | |
Data in XML | ![]() | 27.5 KB | Display | |
Data in CIF | ![]() | 41 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6hzoC ![]() 6hzqC ![]() 6hzrC ![]() 6i1eC ![]() 6i1iC ![]() 6r3xC ![]() 6r40C ![]() 6r42C ![]() 4u3tS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36496.531 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: penA / Production host: ![]() ![]() References: UniProt: E5KLA8, UniProt: P08149*PLUS, serine-type D-Ala-D-Ala carboxypeptidase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.67 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 1 M sodium citrate and 0.1 M sodium cacodylate pH 6.5 |
-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: Feb 5, 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: 1.43→56.01 Å / Num. obs: 115424 / % possible obs: 96.1 % / Redundancy: 4.1 % / Rrim(I) all: 0.189 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 1.43→1.45 Å / Num. unique obs: 5082 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4u3t Resolution: 1.43→56.01 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.917 / SU B: 3.474 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 16.682 Å2
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Refinement step | Cycle: LAST / Resolution: 1.43→56.01 Å
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Refine LS restraints |
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