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Open data
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Basic information
Entry | Database: PDB / ID: 3zlk | |||||||||
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Title | Pseudomonas aeruginosa RmlA in complex with allosteric inhibitor | |||||||||
![]() | GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE | |||||||||
![]() | TRANSFERASE | |||||||||
Function / homology | ![]() 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 | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Alphey, M.S. / Pirrie, L. / Torrie, L.S. / Gardiner, M. / Sarkar, A. / Brenk, R. / Westwood, N.J. / Gray, D. / Naismith, J.H. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 253.5 KB | Display | ![]() |
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PDB format | ![]() | 205.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 51.5 KB | Display | |
Data in CIF | ![]() | 72.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3zllC ![]() 4arwSC ![]() 4asjC ![]() 4asyC ![]() 4b2wC ![]() 4b2xC ![]() 4b3uC ![]() 4b42C ![]() 4b4bC ![]() 4b4gC ![]() 4b4mC ![]() 4b5bC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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
#1: Protein | Mass: 33664.121 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: G3XCK4, UniProt: Q9HU22*PLUS, 1L-myo-inositol 1-phosphate cytidylyltransferase #2: Chemical | ChemComp-Y46 / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.3 % / Description: NONE |
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Crystal grow | pH: 6 Details: 4% PEG6000, 0.1M MES PH6, 0.05M MGCL2, 0.1M NABR, 1% B-ME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 28, 2011 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→37.23 Å / Num. obs: 81490 / % possible obs: 85.5 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 28.17 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2 / % possible all: 69 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4ARW Resolution: 1.952→37.233 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.863 / SU B: 5.056 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.211 / 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: 30.897 Å2
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Refinement step | Cycle: LAST / Resolution: 1.952→37.233 Å
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Refine LS restraints |
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