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- PDB-3vcy: Structure of MurA (UDP-N-acetylglucosamine enolpyruvyl transferas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3vcy | ||||||
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Title | Structure of MurA (UDP-N-acetylglucosamine enolpyruvyl transferase), from Vibrio fischeri in complex with substrate UDP-N-acetylglucosamine and the drug fosfomycin. | ||||||
![]() | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | ||||||
![]() | TRANSFERASE/ANTIBIOTIC / MurA / fosfomycin / peptidoglycan / Amino sugar and nucleotide sugar metabolism / Peptidoglycan biosynthesis / Cytosol / TRANSFERASE-ANTIBIOTIC complex | ||||||
Function / homology | ![]() UDP-N-acetylglucosamine 1-carboxyvinyltransferase / UDP-N-acetylglucosamine 1-carboxyvinyltransferase activity / UDP-N-acetylgalactosamine biosynthetic process / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bensen, D.C. / Rodriguez, S. / Nix, J. / Cunningham, M.L. / Tari, L.W. | ||||||
![]() | ![]() Title: Structure of MurA (UDP-N-acetylglucosamine enolpyruvyl transferase) from Vibrio fischeri in complex with substrate UDP-N-acetylglucosamine and the drug fosfomycin. Authors: Bensen, D.C. / Rodriguez, S. / Nix, J. / Cunningham, M.L. / Tari, L.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 345.3 KB | Display | ![]() |
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PDB format | ![]() | 279.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 74.8 KB | Display | |
Data in CIF | ![]() | 107.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3lthS 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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4 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 45800.199 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: B5F9P4, UDP-N-acetylglucosamine 1-carboxyvinyltransferase |
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-Non-polymers , 5 types, 1187 molecules ![](data/chem/img/FFQ.gif)
![](data/chem/img/UD1.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/UD1.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FFQ / [( #3: Chemical | ChemComp-UD1 / #4: Chemical | ChemComp-PO4 / #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | THE UNBOUND FORM OF THE ANTIBIOTIC IS FOSFOMYCIN. UPON REACTION WITH PROTEIN, IT COVALENTLY BINDS ...THE UNBOUND FORM OF THE ANTIBIOTIC |
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Sequence details | AUTHOR STATES THAT THE AMINO ACID CHANGE AT THIS POSITION WAS THE RESULT OF A RESTRICTION ENZYME ...AUTHOR STATES THAT THE AMINO ACID CHANGE AT THIS POSITION WAS THE RESULT OF A RESTRICTIO |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.81 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25 %(w/v) PEG 4000, 0.1 M BIS-TRIS pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298 K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Oct 13, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→27.9 Å / Num. all: 122583 / Num. obs: 122583 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 4.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3LTH Resolution: 1.925→27.9 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.903 / SU B: 4.781 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 25.476 Å2
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Refinement step | Cycle: LAST / Resolution: 1.925→27.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.925→1.975 Å / Total num. of bins used: 20
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