+Open data
-Basic information
Entry | Database: PDB / ID: 4b3u | ||||||
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Title | Pseudomonas aeruginosa RmlA in complex with allosteric inhibitor | ||||||
Components | GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / THYMIDYLYLTRANSFERASE / ALLOSTERIC INHIBITOR | ||||||
Function / homology | Function and homology information glucose-1-phosphate thymidylyltransferase / glucose-1-phosphate thymidylyltransferase activity / dTDP-rhamnose biosynthetic process / lipopolysaccharide core region biosynthetic process / extracellular polysaccharide biosynthetic process / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Alphey, M.S. / Pirrie, L. / Torrie, L.S. / Gardiner, M. / Sarkar, A. / Brenk, R. / Westwood, N.J. / Gray, D. / Naismith, J.H. | ||||||
Citation | Journal: ACS Chem. Biol. / Year: 2013 Title: Allosteric competitive inhibitors of the glucose-1-phosphate thymidylyltransferase (RmlA) from Pseudomonas aeruginosa. Authors: Alphey, M.S. / Pirrie, L. / Torrie, L.S. / Boulkeroua, W.A. / Gardiner, M. / Sarkar, A. / Maringer, M. / Oehlmann, W. / Brenk, R. / Scherman, M.S. / McNeil, M. / Rejzek, M. / Field, R.A. / ...Authors: Alphey, M.S. / Pirrie, L. / Torrie, L.S. / Boulkeroua, W.A. / Gardiner, M. / Sarkar, A. / Maringer, M. / Oehlmann, W. / Brenk, R. / Scherman, M.S. / McNeil, M. / Rejzek, M. / Field, R.A. / Singh, M. / Gray, D. / Westwood, N.J. / Naismith, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b3u.cif.gz | 260.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b3u.ent.gz | 210.7 KB | Display | PDB format |
PDBx/mmJSON format | 4b3u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/4b3u ftp://data.pdbj.org/pub/pdb/validation_reports/b3/4b3u | HTTPS FTP |
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-Related structure data
Related structure data | 3zlkC 3zllC 4arwSC 4asjC 4asyC 4b2wC 4b2xC 4b42C 4b4bC 4b4gC 4b4mC 4b5bC 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 33664.121 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Plasmid: PET23A MODIFIED / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: Q9HU22, glucose-1-phosphate thymidylyltransferase |
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-Non-polymers , 5 types, 818 molecules
#2: Chemical | ChemComp-NWL / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-MES / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.9 % / Description: NONE |
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Crystal grow | pH: 6 Details: 4% PEG 6000, 0.1 M MES PH 6, 0.05 M MGCL2, 0.1 M NA BR, 1% BETA-MERCAPTOETHANOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→45.13 Å / Num. obs: 118780 / % possible obs: 91.1 % / Observed criterion σ(I): 1.5 / Redundancy: 3.3 % / Biso Wilson estimate: 27.37 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.75→1.8 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.7 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4ARW Resolution: 1.8→45.129 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.91 / SU B: 4.061 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.163 / 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 / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.148 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→45.129 Å
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Refine LS restraints |
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