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Open data
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Basic information
Entry | Database: PDB / ID: 7b61 | ||||||
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Title | Crystal structure of MurE from E.coli in complex with Z57299526 | ||||||
![]() | 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 | ||||||
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. / Talon, R. / Douangamath, A. / 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. / Talon, R. / Douangamath, A. / 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 | ![]() | 203.8 KB | Display | ![]() |
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PDB format | ![]() | 160.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 943.8 KB | Display | ![]() |
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Full document | ![]() | 954.9 KB | Display | |
Data in XML | ![]() | 39 KB | Display | |
Data in CIF | ![]() | 55.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7b53SC ![]() 7b60C ![]() 7b68C ![]() 7b6gC ![]() 7b6iC ![]() 7b6jC ![]() 7b6kC ![]() 7b6lC ![]() 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
-Protein , 1 types, 2 molecules AB
#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 |
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-Non-polymers , 6 types, 365 molecules ![](data/chem/img/CIT.gif)
![](data/chem/img/SYQ.gif)
![](data/chem/img/T3Z.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SYQ.gif)
![](data/chem/img/T3Z.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-IPA / #6: Chemical | ChemComp-DMS / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.12 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M citrate pH 5.5 17% PEG4K 22% 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: Jul 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→73.38 Å / Num. obs: 124106 / % possible obs: 94.9 % / Redundancy: 1.7 % / CC1/2: 0.997 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.57→1.65 Å / Num. unique obs: 18002 / CC1/2: 0.427 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7B53 Resolution: 1.65→56.09 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.669 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.71 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→56.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
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