+Open data
-Basic information
Entry | Database: PDB / ID: 6tqg | ||||||
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Title | Pseudomonas aeruginosa RmlA in complex with allosteric inhibitor | ||||||
Components | Glucose-1-phosphate thymidylyltransferase | ||||||
Keywords | TRANSFERASE / RmlA / allostery / thymidylyltransferase / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å | ||||||
Authors | Alphey, M.S. / Xiao, G. / Westwood, J.N. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Bioorg.Med.Chem. / Year: 2021 Title: Next generation Glucose-1-phosphate thymidylyltransferase (RmlA) inhibitors: An extended SAR study to direct future design. Authors: Xiao, G. / Alphey, M.S. / Tran, F. / Pirrie, L. / Milbeo, P. / Zhou, Y. / Bickel, J.K. / Kempf, O. / Kempf, K. / Naismith, J.H. / Westwood, N.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tqg.cif.gz | 428.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tqg.ent.gz | 353.7 KB | Display | PDB format |
PDBx/mmJSON format | 6tqg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tq/6tqg ftp://data.pdbj.org/pub/pdb/validation_reports/tq/6tqg | HTTPS FTP |
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-Related structure data
Related structure data | 6t37C 6t38C 5ftvS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Refine code: 0
NCS ensembles :
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-Components
#1: Protein | Mass: 33664.121 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Residues missing from the model due to missing electron density resulting from loop/sidechain flexibility Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: rmlA, rfbA, CAZ10_00575, E4V10_15605, IPC1492_24235, IPC605_02475, PAMH19_2921 Production host: Escherichia coli (E. coli) References: UniProt: G3XCK4, UniProt: Q9HU22*PLUS, glucose-1-phosphate thymidylyltransferase #2: Chemical | ChemComp-NVQ / ~{ #3: Chemical | ChemComp-MES / #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.79 Å3/Da / Density % sol: 55.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 11% PEG 6000, 0.15M MES pH6, 0.15M sodium bromide, 0.15M magnesium chloride, 1% B-mercaptoethanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5417 Å | ||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 3, 2019 / Details: mirrors | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5417 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.45→29.57 Å / Num. obs: 49961 / % possible obs: 95.6 % / Redundancy: 5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.071 / Rrim(I) all: 0.164 / Net I/σ(I): 7.9 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.585
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5FTV Resolution: 2.45→29.57 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.885 / SU B: 22.571 / SU ML: 0.265 / SU R Cruickshank DPI: 0.5301 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.53 / ESU R Free: 0.306 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.02 Å2 / Biso mean: 46.12 Å2 / Biso min: 12.55 Å2
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Refinement step | Cycle: final / Resolution: 2.45→29.57 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.45→2.514 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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