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Open data
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Basic information
Entry | Database: PDB / ID: 7b6l | ||||||
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Title | Crystal structure of MurE from E.coli in complex with Z57299368 | ||||||
![]() | UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase | ||||||
![]() | BIOSYNTHETIC PROTEIN / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2 / 6-diaminopimelate ligase cell wall biosynthesis ligase drug target / Structural Genomics / Structural Genomics Consortium / SGC / fragment screening | ||||||
Function / homology | ![]() UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase / UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / magnesium ion binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Koekemoer, L. / Steindel, M. / Fairhead, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / von Delft, F. / Krojer, T. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Crystal structure of MurE from E.coli Authors: Koekemoer, L. / Steindel, M. / Fairhead, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / von Delft, F. / Krojer, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 378.3 KB | Display | ![]() |
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PDB format | ![]() | 309.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 35.3 KB | Display | |
Data in CIF | ![]() | 49.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7b53SC ![]() 7b60C ![]() 7b61C ![]() 7b68C ![]() 7b6gC ![]() 7b6iC ![]() 7b6jC ![]() 7b6kC ![]() 7b6mC ![]() 7b6nC ![]() 7b6oC ![]() 7b6pC ![]() 7b6qC ![]() 7b9eC ![]() 7b9wC 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: 53493.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: murE, b0085, JW0083 / Plasmid: pNIC28-Bsa4 Details (production host): N-terminal His6-tag -Twin-Strep-tag II -TEV-cleavage site Production host: ![]() ![]() References: UniProt: P22188, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.64 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M citrate pH 5.5 13% PEG4K 21% 2-propanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 2, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→73.82 Å / Num. obs: 53195 / % possible obs: 93 % / Redundancy: 2 % / CC1/2: 0.998 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.07→2.18 Å / Num. unique obs: 8015 / CC1/2: 0.447 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7B53 Resolution: 2.08→73.82 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / SU B: 17.155 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.125 Å2
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Refinement step | Cycle: LAST / Resolution: 2.08→73.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.08→2.134 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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