+Open data
-Basic information
Entry | Database: PDB / ID: 4e1k | ||||||
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Title | GlmU in complex with a Quinazoline Compound | ||||||
Components | Bifunctional protein GlmU | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / peptidoglycan synthesis / cell shape / metal-binding / cell wall biogenesis/degradation / multifunctional enzyme / acyltransferase / uridyltransferase / Nucleotidyl transferase / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Larsen, N.A. / Doig, P. | ||||||
Citation | Journal: Biochem.J. / Year: 2012 Title: An aminoquinazoline inhibitor of the essential bacterial cell wall synthetic enzyme GlmU has a unique non-protein-kinase-like binding mode. Authors: Larsen, N.A. / Nash, T.J. / Morningstar, M. / Shapiro, A.B. / Joubran, C. / Blackett, C.J. / Patten, A.D. / Boriack-Sjodin, P.A. / Doig, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4e1k.cif.gz | 193.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e1k.ent.gz | 154.7 KB | Display | PDB format |
PDBx/mmJSON format | 4e1k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/4e1k ftp://data.pdbj.org/pub/pdb/validation_reports/e1/4e1k | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 49346.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: glmU, HI_0642 / Production host: Escherichia coli (E. coli) References: UniProt: P43889, UDP-N-acetylglucosamine diphosphorylase, glucosamine-1-phosphate N-acetyltransferase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-PG4 / | #4: Chemical | ChemComp-0N5 / | #5: 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: 3.75 Å3/Da / Density % sol: 67.2 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: 1.6-1.8 M ammonium sulfate and 0.1 M MES pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 5, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→61.4 Å / Num. all: 46600 / Num. obs: 46480 / % possible obs: 92.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.8 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 1.8 / % possible all: 62 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→54.55 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.103 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.176 / 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: 50.673 Å2
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Refinement step | Cycle: LAST / Resolution: 2→54.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 15.648 Å / Origin y: 10.965 Å / Origin z: 72.421 Å
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Refinement TLS group |
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