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- PDB-8evy: DdlB from Pseudomonas aeruginosa PAO1 in complex with ATP and D-a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8evy | ||||||
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Title | DdlB from Pseudomonas aeruginosa PAO1 in complex with ATP and D-ala-D-ala | ||||||
![]() | D-alanine--D-alanine ligase B | ||||||
![]() | LIGASE/PRODUCT / ATP-grasp / LIGASE / LIGASE-PRODUCT complex | ||||||
Function / homology | ![]() D-alanine-D-alanine ligase / D-alanine-D-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Pederick, J.L. / Woolman, J.C. / Bruning, J.B. | ||||||
Funding support | 1items
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![]() | ![]() Title: Comparative functional and structural analysis of Pseudomonas aeruginosa d-alanine-d-alanine ligase isoforms as prospective antibiotic targets. Authors: Pederick, J.L. / Woolman, J.C. / Bruning, J.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 198.1 KB | Display | ![]() |
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PDB format | ![]() | 155.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 36.3 KB | Display | |
Data in CIF | ![]() | 49.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8evvC ![]() 8evwSC ![]() 8evxC ![]() 8evzC C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 3 molecules BAC
#1: Protein | Mass: 34486.297 Da / Num. of mol.: 3 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: ddlB, PA4410 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 248 molecules ![](data/chem/img/DAL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-DAL / #3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.81 Å3/Da / Density % sol: 67.74 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop Details: 0.1M Tris pH 7.8, 5% gamma-PGA (Na+ form, LM) , 30% PEG 500 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 17, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→39.8 Å / Num. obs: 66359 / % possible obs: 100 % / Redundancy: 13.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.043 / Rrim(I) all: 0.161 / Χ2: 0.96 / Net I/σ(I): 13.7 / Num. measured all: 920367 |
Reflection shell | Resolution: 2.35→2.41 Å / % possible obs: 99.9 % / Redundancy: 14.4 % / Rmerge(I) obs: 1.944 / Num. measured all: 63556 / Num. unique obs: 4413 / CC1/2: 0.699 / Rpim(I) all: 0.529 / Rrim(I) all: 2.016 / Χ2: 0.86 / Net I/σ(I) obs: 1.5 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8EVW Resolution: 2.35→39.8 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.69 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→39.8 Å
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Refine LS restraints |
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LS refinement shell |
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