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Yorodumi- PDB-1fxo: THE STRUCTURAL BASIS OF THE CATALYTIC MECHANISM AND REGULATION OF... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fxo | ||||||
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Title | THE STRUCTURAL BASIS OF THE CATALYTIC MECHANISM AND REGULATION OF GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE (RMLA). TMP COMPLEX. | ||||||
Components | GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / 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 / SYNCHROTRON / Phase extension in direct method / Resolution: 1.66 Å | ||||||
Authors | Blankenfeldt, W. / 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: To be Published 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. / 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 | 1fxo.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1fxo.ent.gz | 899.4 KB | Display | PDB format |
PDBx/mmJSON format | 1fxo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fxo_validation.pdf.gz | 7.6 MB | Display | wwPDB validaton report |
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Full document | 1fxo_full_validation.pdf.gz | 7.8 MB | Display | |
Data in XML | 1fxo_validation.xml.gz | 137.5 KB | Display | |
Data in CIF | 1fxo_validation.cif.gz | 197.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fx/1fxo ftp://data.pdbj.org/pub/pdb/validation_reports/fx/1fxo | HTTPS FTP |
-Related structure data
Related structure data | 1fzwC 1g0rC 1g1lC 1g23SC 1g2vC 1g3lC 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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1 |
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2 |
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Unit cell |
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Details | The biological assembly is a tetramer consisting of chains A,B,C and D or E,F,G and H, respectively. |
-Components
#1: Protein | Mass: 32488.844 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Plasmid: PET23A(+) / Production host: Escherichia coli (E. coli) References: UniProt: Q9HU22, glucose-1-phosphate thymidylyltransferase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-TMP / #4: Water | ChemComp-HOH / | Compound details | RmlA in complex with thymidine-5'-phosphate (TMP). TMP binds the active centre in two alternative ...RmlA in complex with thymidine-5'-phosphate (TMP). TMP binds the active centre in two alternative conformations. | |
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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: 2.54 Å3/Da / Density % sol: 54.9 % | ||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 10 % PEG 6000, 0.1 M sodium citrate, 0.5 M lithium sulfate, 4 microlitre protein, 4 microlitre precipitant, 1 microlitre 50 mM TMP, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 292K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 KDetails: Blankenfeldt, W., (2000) Acta Crystallogr.,Sect.D, 56, 1501. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 3, 2000 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→32.12 Å / Num. all: 297160 / Num. obs: 1141819 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.052 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.66→1.74 Å / Redundancy: 2 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 2 / Num. unique all: 75372 / Rsym value: 0.332 / % possible all: 81.2 |
Reflection | *PLUS Num. obs: 297160 / Num. measured all: 1141819 |
Reflection shell | *PLUS % possible obs: 81.2 % |
-Processing
Software |
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Refinement | Method to determine structure: Phase extension in direct method Starting model: MAD structure (1G23) Resolution: 1.66→73 Å / SU B: 5.39619 / SU ML: 0.09328 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.68841 / ESU R Free: 0.12821 / Stereochemistry target values: Engh and Huber Details: Used TLS-option in refmac5. Anisotropic B-factors were calculated but not refined (ncycle 0).
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Displacement parameters | Biso mean: 14.14 Å2
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Refinement step | Cycle: LAST / Resolution: 1.66→73 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.303 / Rfactor Rwork: 0.225 |