+Open data
-Basic information
Entry | Database: PDB / ID: 4y7v | |||||||||
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Title | Structural analysis of MurU | |||||||||
Components | Nucleotidyl transferaseNucleotidyltransferase | |||||||||
Keywords | TRANSFERASE / Nucleotidyltransferase family protein / uridyltransferase / Rossman fold / MurNAc-1P | |||||||||
Function / homology | Function and homology information N-acetylmuramic acid metabolic process / N-acetyl-alpha-D-muramate 1-phosphate uridylyltransferase / uridylyltransferase activity / peptidoglycan turnover / carbohydrate derivative binding / UTP binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic / magnesium ion binding Similarity search - Function | |||||||||
Biological species | Pseudomonas putida (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å | |||||||||
Authors | Renner-Schneck, M.G. / Stehle, T. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Crystal Structure of the N-Acetylmuramic Acid alpha-1-Phosphate (MurNAc-alpha 1-P) Uridylyltransferase MurU, a Minimal Sugar Nucleotidyltransferase and Potential Drug Target Enzyme in Gram-negative Pathogens. Authors: Renner-Schneck, M. / Hinderberger, I. / Gisin, J. / Exner, T. / Mayer, C. / Stehle, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y7v.cif.gz | 101.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y7v.ent.gz | 78.2 KB | Display | PDB format |
PDBx/mmJSON format | 4y7v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/4y7v ftp://data.pdbj.org/pub/pdb/validation_reports/y7/4y7v | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | biological unit is the same as asym. |
-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 24913.369 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (strain BIRD-1) (bacteria) Strain: BIRD-1 / Gene: PPUBIRD1_0444 / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / References: UniProt: E4RE40, UniProt: Q88QT2*PLUS |
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#4: Sugar | ChemComp-491 / |
-Non-polymers , 4 types, 70 molecules
#2: Chemical | ChemComp-GOL / |
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#3: Chemical | ChemComp-SO4 / |
#5: Chemical | ChemComp-2PN / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: (NH4)2SO4, MES |
-Data collection
Diffraction | Mean temperature: 93.2 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 18, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 24133 / % possible obs: 99.9 % / Redundancy: 20 % / Net I/σ(I): 27.7 |
Reflection shell | Resolution: 1.8→1.85 Å / Mean I/σ(I) obs: 0.91 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Resolution: 1.8→49.615 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.81 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 121.35 Å2 / Biso mean: 52.21 Å2 / Biso min: 20 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→49.615 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 / % reflection obs: 100 %
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