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Yorodumi- PDB-2v0i: Characterization of Substrate Binding and Catalysis of the Potent... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v0i | ||||||
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Title | Characterization of Substrate Binding and Catalysis of the Potential Antibacterial Target N-acetylglucosamine-1-phosphate Uridyltransferase (GlmU) | ||||||
Components | BIFUNCTIONAL PROTEIN GLMU | ||||||
Keywords | TRANSFERASE / CELL WALL / CELL SHAPE / PEPTIDOGLYCAN ASSOCIATIVE MECHANISM / MULTIFUNCTIONAL ENZYME / NUCLEOTIDYLTRANSFERASE / URIDYLATION / METAL-BINDING / ACYLTRANSFERASE | ||||||
Function / homology | Function and homology information glucosamine-1-phosphate N-acetyltransferase / glucosamine-1-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / lipid A biosynthetic process / peptidoglycan biosynthetic process / cell wall organization / cell morphogenesis / regulation of cell shape ...glucosamine-1-phosphate N-acetyltransferase / glucosamine-1-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / lipid A biosynthetic process / peptidoglycan biosynthetic process / cell wall organization / cell morphogenesis / regulation of cell shape / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | HAEMOPHILUS INFLUENZAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | Mochalkin, I. / Lightle, S. / Ohren, J.F. / Chirgadze, N.Y. | ||||||
Citation | Journal: Protein Sci. / Year: 2007 Title: Characterization of Substrate Binding and Catalysis in the Potential Antibacterial Target N-Acetylglucosamine-1-Phosphate Uridyltransferase (Glmu). Authors: Mochalkin, I. / Lightle, S. / Zhu, Y. / Ohren, J.F. / Spessard, C. / Chirgadze, N.Y. / Banotai, C. / Melnick, M. / Mcdowell, L. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v0i.cif.gz | 110.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v0i.ent.gz | 83.6 KB | Display | PDB format |
PDBx/mmJSON format | 2v0i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v0/2v0i ftp://data.pdbj.org/pub/pdb/validation_reports/v0/2v0i | HTTPS FTP |
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-Related structure data
Related structure data | 2v0hSC 2v0jC 2v0kC 2v0lC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 49346.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HAEMOPHILUS INFLUENZAE (bacteria) / References: UniProt: P43889, Transferases |
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-Non-polymers , 5 types, 314 molecules
#2: Chemical | ChemComp-UD1 / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-SO4 / #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: 3.65 Å3/Da / Density % sol: 66.06 % / Description: NONE |
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Crystal grow | pH: 6 Details: 1.2-1.8M AMMONIUM SULFATE, 2%PEG-400, 0.1M MES PH 5.2-6.1, 20 MM MGCL2, 10 MM UDP-GLCNAC |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 1, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 64262 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 37.9 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.5 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V0H Resolution: 1.89→119.52 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.054 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.102 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.81 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→119.52 Å
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Refine LS restraints |
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