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Yorodumi- PDB-1g3l: THE STRUCTURAL BASIS OF THE CATALYTIC MECHANISM AND REGULATION OF... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g3l | ||||||
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Title | THE STRUCTURAL BASIS OF THE CATALYTIC MECHANISM AND REGULATION OF GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE (RMLA). TDP-L-RHAMNOSE COMPLEX. | ||||||
Components | GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / L-RHAMNOSE / NUCLEOTIDYLTRANSFERASE / PYROPHOSPHORYLASE / THYMIDYLYLTRANSFERASE / ALLOSTERY | ||||||
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 / Resolution: 2.7 Å | ||||||
Authors | Blankenfeldt, W. / Asuncion, M. / Lam, J.S. / Naismith, J.H. | ||||||
Citation | Journal: EMBO J. / Year: 2000 Title: The structural basis of the catalytic mechanism and regulation of glucose-1-phosphate thymidylyltransferase (RmlA). Authors: Blankenfeldt, W. / Asuncion, M. / Lam, J.S. / Naismith, J.H. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: The Purification, Crystallisation and Preliminary Structural Characterisation of Glucose-1-Phosphate Thymidylyltransferase (Rmla), the First Enzyme of the Dtdp-L-Rhamnose Synthesis Pathway ...Title: The Purification, Crystallisation and Preliminary Structural Characterisation of Glucose-1-Phosphate Thymidylyltransferase (Rmla), the First Enzyme of the Dtdp-L-Rhamnose Synthesis Pathway from Pseudomonas Aeruginosa Authors: Blankenfeldt, W. / Giraud, M.F. / Leonard, G. / Rahim, R. / Creuzenet, C. / Lam, J.S. / Naismith, J.H. #2: Journal: J.Biol.Chem. / Year: 1965 Title: The Nucleotide Specificity and Feedback Control of Thymidine Diphosphate D-Glucose Pyrophosphorylase. Authors: Melo, A. / Glaser, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g3l.cif.gz | 235.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g3l.ent.gz | 192.3 KB | Display | PDB format |
PDBx/mmJSON format | 1g3l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1g3l_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 1g3l_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 1g3l_validation.xml.gz | 48.7 KB | Display | |
Data in CIF | 1g3l_validation.cif.gz | 62.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/1g3l ftp://data.pdbj.org/pub/pdb/validation_reports/g3/1g3l | HTTPS FTP |
-Related structure data
Related structure data | 1fxoC 1fzwC 1g0rC 1g1lSC 1g23C 1g2vC 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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1 |
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Unit cell |
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Details | The biological assembly is a tetramer consisting of two dimers. |
-Components
#1: Protein | Mass: 32488.844 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Plasmid: PET23A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(LAMBDA DE3) References: UniProt: Q9HU22, glucose-1-phosphate thymidylyltransferase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-TRH / |
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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: 2.55 Å3/Da / Density % sol: 45.2 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 10 % (w/v) PEG 6000, 0.2 M Li-sulfate, 0.1 M Na-citrate pH 4.0; protein incubated with 10 mM dTDP-L-rhamnose, VAPOR DIFFUSION, SITTING DROP, temperature 292K | ||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Mar 1, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→49.9 Å / Num. obs: 36311 / % possible obs: 94.2 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 37.11 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.8→2.84 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 2.9 / % possible all: 70.8 |
Reflection | *PLUS Num. measured all: 260832 |
Reflection shell | *PLUS % possible obs: 70.8 % |
-Processing
Software |
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Refinement | Starting model: 1G1L Resolution: 2.7→100 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.47
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Displacement parameters | Biso mean: 12.78 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→100 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.333 / Rfactor Rwork: 0.255 |