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Open data
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Basic information
Entry | Database: PDB / ID: 1e0d | ||||||
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Title | UDP-N-Acetylmuramoyl-L-Alanine:D-Glutamate Ligase | ||||||
![]() | UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE | ||||||
![]() | LIGASE / PEPTIDOGLYCAN SYNTHESIS / MURD / ADP-FORMING ENZYME | ||||||
Function / homology | ![]() UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase / UDP-N-acetylmuramoylalanine-D-glutamate ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / ATP binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fanchon, E. / Bertrand, J. / Chantalat, L. / Dideberg, O. | ||||||
![]() | ![]() Title: "Open" Structures of Murd: Domain Movements and Structural Similarities with Folylpolyglutamate Synthetase. Authors: Bertrand, J. / Fanchon, E. / Martin, L. / Chantalat, L. / Auger, G. / Blanot, D. / Van Heijenoort, J. / Dideberg, O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 98.5 KB | Display | ![]() |
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PDB format | ![]() | 74 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 377.1 KB | Display | ![]() |
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Full document | ![]() | 391.5 KB | Display | |
Data in XML | ![]() | 11.4 KB | Display | |
Data in CIF | ![]() | 18.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1eehC ![]() 1uagS 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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Unit cell |
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Components
#1: Protein | Mass: 46889.250 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P14900, UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.96 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 / Details: pH 6.00 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 15 ℃ / pH: 7.5 / Method: vapor diffusion, hanging dropDetails: drop solution was mixed with an equal volume of reservoir solution | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 23, 1997 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 19294 / % possible obs: 99 % / Redundancy: 7.3 % / Biso Wilson estimate: 25.5 Å2 / Rsym value: 0.04 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.4→2.8 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.21 / % possible all: 99.9 |
Reflection | *PLUS % possible obs: 98.9 % / Rmerge(I) obs: 0.088 |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.212 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2 DOMAINS FROM 1UAG Resolution: 2.4→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1911015.04 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: RESIDUES 183-188 AND 221 - 222 WERE NOT VISIBLE IN THE ELECTRON DENSITY AND THEIR COORDINATES ARE NOT INCLUDED IN THIS ENTRY. RESIDUES 183-188 AND 221 - 222 WERE NOT VISIBLE IN THE ELECTRON ...Details: RESIDUES 183-188 AND 221 - 222 WERE NOT VISIBLE IN THE ELECTRON DENSITY AND THEIR COORDINATES ARE NOT INCLUDED IN THIS ENTRY. RESIDUES 183-188 AND 221 - 222 WERE NOT VISIBLE IN THE ELECTRON DENSITY AND THEIR COORDINATES ARE NOT INCLUDED IN THIS ENTRY.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 63.2219 Å2 / ksol: 0.365383 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 40.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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