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Open data
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Basic information
Entry | Database: PDB / ID: 5fuh | ||||||
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Title | Pseudomonas aeruginosa RmlA in complex with allosteric inhibitor | ||||||
![]() | GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE | ||||||
![]() | TRANSFERASE / THYMIDYLYL / ALLOSTERIC / INHIBITOR / PSEUDOMONAS | ||||||
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. / Tran, F. / Westwood, N.J. / Naismith, J.H. | ||||||
![]() | ![]() Title: Allosteric Competitive Inhibitors of the Glucose-1-Phosphate Thymidylyltransferase (Rmla) from Pseudomonas Aeruginosa. Authors: Tran, F. / Alphey, M.S. / 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 | ![]() | 254.3 KB | Display | ![]() |
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PDB format | ![]() | 207 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 50.6 KB | Display | |
Data in CIF | ![]() | 69.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ftsC ![]() 5ftvC ![]() 5fu0C ![]() 5fu8C ![]() 5fyeC ![]() 4asjS 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
-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.) ![]() ![]() ![]() ![]() References: UniProt: Q9HU22, glucose-1-phosphate thymidylyltransferase |
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-Non-polymers , 5 types, 588 molecules ![](data/chem/img/HKX.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HKX / #3: Chemical | ChemComp-MES / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | N-TERMINAL HIS-TAG PRESENT |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.58 % / 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: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2014 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→67.35 Å / Num. obs: 175397 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.59→1.63 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.1 / % possible all: 96.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4ASJ Resolution: 1.6→67.349 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.997 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME RESIDUES AT THE N-TERMINUS ARE DISORDERED. SOME RESIDUES HAVE BEEN MODELLED IN MULTIPLE CONFORMATIONS. THE BOUND INHIBITOR HAS PARTIAL ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME RESIDUES AT THE N-TERMINUS ARE DISORDERED. SOME RESIDUES HAVE BEEN MODELLED IN MULTIPLE CONFORMATIONS. THE BOUND INHIBITOR HAS PARTIAL OCCUPANCY. SOME EXTRA ELECTRON DENSITY IS OBSERVED IN THE PARTIALLY OCCUPIED INHIBITOR BINDING SITE, MOST LIKELY DUE TO WATERS BOUND WHEN INHIBITOR IS ABSENT. SOME EXTRA ELECTRON DENSITY IS OBSERVED NEAR THE MULTIPLE CONFORMATIONS OF GLN237, MOST LIKELY DUE TO WATERS BOUND WHEN SIDE CHAIN IS IN ALTERNATIVE CONFORMATION.
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Solvent computation | Ion probe radii: 0.4 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.619 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→67.349 Å
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Refine LS restraints |
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