+Open data
-Basic information
Entry | Database: PDB / ID: 4aaw | ||||||
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Title | S.pneumoniae GlmU in complex with an antibacterial inhibitor | ||||||
Components | BIFUNCTIONAL PROTEIN GLMU | ||||||
Keywords | 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 | STREPTOCOCCUS PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Otterbein, L. / Breed, J. / Ogg, D.J. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2012 Title: Inhibitors of Acetyltransferase Domain of N-Acetylglucosamine-1-Phosphate-Uridyltransferase/ Glucosamine-1-Phosphate-Acetyltransferase (Glmu). Part 1: Hit to Lead Evaluation of a Novel Arylsulfonamide Series. Authors: Green, O.M. / McKenzie, A.R. / Shapiro, A.B. / Otterbein, L. / Ni, H. / Patten, A. / Stokes, S. / Albert, R. / Kawatkar, S. / Breed, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4aaw.cif.gz | 189.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4aaw.ent.gz | 151 KB | Display | PDB format |
PDBx/mmJSON format | 4aaw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/4aaw ftp://data.pdbj.org/pub/pdb/validation_reports/aa/4aaw | HTTPS FTP |
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-Related structure data
Related structure data | 4aa7C 4ac3C 1g97S C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 49481.469 Da / Num. of mol.: 1 / Fragment: BIFUNCTIONAL GLMU Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Plasmid: PBA989 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): HMS174 (DE3) References: UniProt: Q8DQ18, glucosamine-1-phosphate N-acetyltransferase, UDP-N-acetylglucosamine diphosphorylase |
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#2: Chemical | ChemComp-R84 / |
#3: Chemical | ChemComp-SO4 / |
#4: 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: 4.7 Å3/Da / Density % sol: 67 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 18-23% PEG 3350, 0.2 M AMMONIUM SULPHATE, 25 MM TRIS-HCL, PH 7.5, 50 MM NACL, 2 MM TCEP |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 28, 2006 / Details: SILICON TOROIDAL MIRROR COATED WITH RHODIUM |
Radiation | Monochromator: SILICON (1 1 1) CHANNEL- CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→76.5 Å / Num. obs: 74324 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.26 / Net I/σ(I): 2.2 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.1 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1G97 Resolution: 2.2→76.47 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.912 / SU B: 8.441 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.077 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→76.47 Å
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