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- PDB-5a5f: CRYSTAL STRUCTURE OF MURD LIGASE FROM ESCHERICHIA COLI IN COMPLEX... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5a5f | ||||||
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Title | CRYSTAL STRUCTURE OF MURD LIGASE FROM ESCHERICHIA COLI IN COMPLEX WITH UMA AND ADP | ||||||
![]() | UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE | ||||||
![]() | LIGASE / PEPTIDOGLYCAN SYNTHESIS / ADP-FORMING ENZYME / CELL WALL / CELL SHAPE / CELL CYCLE / NUCLEOTIDE-BINDING / ATP- BINDING / CELL DIVISION / LIGAND / CONFORMATION | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Sink, R. / Kotnik, M. / Zega, A. / Barreteau, H. / Gobec, S. / Blanot, D. / Dessen, A. / Contreras-Martel, C. | ||||||
![]() | ![]() Title: Crystallographic Study of Peptidoglycan Biosynthesis Enzyme MurD: Domain Movement Revisited. Authors: Sink, R. / Kotnik, M. / Zega, A. / Barreteau, H. / Gobec, S. / Blanot, D. / Dessen, A. / Contreras-Martel, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 184 KB | Display | ![]() |
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PDB format | ![]() | 146.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 20.4 KB | Display | |
Data in CIF | ![]() | 30 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5a5eC ![]() 3uagS C: citing same article ( S: Starting model for refinement |
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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: 46976.332 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-UMA / | ||
#3: Chemical | ChemComp-ADP / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.55 % / Description: NONE |
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Crystal grow | pH: 7.4 Details: 4 MG/ML PROTEIN, 1 MM UMA, 5 MM AMP-PNP, 1 MM NAN3, 1 MM DTT, 20 MM HEPES, PH 7.4, 1.8 M NA-MALONATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 30, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97623 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→46.46 Å / Num. obs: 51890 / % possible obs: 98.2 % / Observed criterion σ(I): 3 / Redundancy: 5.4 % / Biso Wilson estimate: 37.009 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.75 |
Reflection shell | Resolution: 1.9→2.01 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 3.22 / % possible all: 94.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3UAG Resolution: 1.9→46.47 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.549 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.207 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→46.47 Å
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Refine LS restraints |
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