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Open data
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Basic information
Entry | Database: PDB / ID: 5fye | ||||||
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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 | ![]() | 244.7 KB | Display | ![]() |
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PDB format | ![]() | 198.9 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 | ![]() | 47.9 KB | Display | |
Data in CIF | ![]() | 64.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ftsC ![]() 5ftvC ![]() 5fu0C ![]() 5fu8C ![]() 5fuhC ![]() 4asjS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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, glucose-1-phosphate thymidylyltransferase #2: Chemical | ChemComp-LD6 / #3: Chemical | ChemComp-MES / #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | 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: 2.57 Å3/Da / Density % sol: 52.13 % / Description: NONE |
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Crystal grow | pH: 6 Details: 4% PEG 6000, 0.1 M MES PH6, 0.05 M MGCL2, 0.1 M 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: Mar 23, 2015 / 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: 2.4→27.8 Å / Num. obs: 48194 / % possible obs: 94.3 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 15.13 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.5 / % possible all: 94.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4ASJ Resolution: 2.4→134.512 Å / Cor.coef. Fo:Fc: 0.841 / Cor.coef. Fo:Fc free: 0.81 / SU B: 10.109 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.704 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME RESIDUES AT THE N-TERMINI ARE DISORDERED AND HAVE BEEN OMITTED FROM THE MODEL. RESIDUES D192-D197 WERE NOT CLEARLY DEFINED AND HAVE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME RESIDUES AT THE N-TERMINI ARE DISORDERED AND HAVE BEEN OMITTED FROM THE MODEL. RESIDUES D192-D197 WERE NOT CLEARLY DEFINED AND HAVE BEEN OMITTED FROM THE MODEL. THE BOUND COMPOUND HAS BEEN MODELLED IN THE PREDOMINANT CONFORMATION. SEVERAL RESIDUES HAVE BEEN MODELLED IN WITH ALTERNATE CONFORMATIONS.
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Solvent computation | Ion probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.002 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→134.512 Å
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Refine LS restraints |
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