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- PDB-7kiv: Crystal structure of Pseudomonas aeruginosa PBP3 in complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7kiv | ||||||
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Title | Crystal structure of Pseudomonas aeruginosa PBP3 in complex with avibactam | ||||||
![]() | Peptidoglycan D,D-transpeptidase FtsI | ||||||
![]() | HYDROLASE/Inhibitor/Antibiotic / Inhibitor / ![]() ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | van den Akker, F. | ||||||
![]() | ![]() Title: Structural Characterization of Diazabicyclooctane beta-Lactam "Enhancers" in Complex with Penicillin-Binding Proteins PBP2 and PBP3 of Pseudomonas aeruginosa. Authors: Rajavel, M. / Kumar, V. / Nguyen, H. / Wyatt, J. / Marshall, S.H. / Papp-Wallace, K.M. / Deshpande, P. / Bhavsar, S. / Yeole, R. / Bhagwat, S. / Patel, M. / Bonomo, R.A. / van den Akker, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.8 KB | Display | ![]() |
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PDB format | ![]() | 78 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7kisC ![]() 7kitC ![]() 7kiwC ![]() 3pbqS 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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Unit cell |
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Components
#1: Protein | Mass: 62933.082 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: ftsI, pbpB, PA4418 / Production host: ![]() ![]() ![]() References: UniProt: G3XD46, ![]() |
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#2: Chemical | ChemComp-NXL / (![]() |
#3: Water | ChemComp-HOH / ![]() |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.11 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30% polyethylene glycol 4000, 0.2 M MgCl2, 0.1 M Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 28, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.389→29.581 Å / Num. obs: 19459 / % possible obs: 99.3 % / Redundancy: 6.3 % / CC1/2: 0.993 / Rmerge(I) obs: 0.196 / Rpim(I) all: 0.09 / Rrim(I) all: 0.227 / Net I/σ(I): 10.9 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3PBQ Resolution: 2.389→29.581 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.6 / 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 max: 90.52 Å2 / Biso mean: 34.9163 Å2 / Biso min: 12.28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.389→29.581 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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