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Yorodumi- PDB-1h5r: Thymidylyltransferase complexed with Thimidine and Glucose-1-phospate -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h5r | ||||||
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Title | Thymidylyltransferase complexed with Thimidine and Glucose-1-phospate | ||||||
Components | (GLUCOSE-1-PHOSPHATE ...Glucose 1-phosphate) x 2 | ||||||
Keywords | TRANSFERASE / PYROPHOSPHATASE / NUCLEOTIDE SUGAR METHABOLISM | ||||||
Function / homology | Function and homology information glucose-1-phosphate thymidylyltransferase / glucose-1-phosphate thymidylyltransferase activity / O antigen biosynthetic process / dTDP-rhamnose biosynthetic process / extracellular polysaccharide biosynthetic process / protein homotetramerization / identical protein binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Rosano, C. / Zuccotti, S. / Bolognesi, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Kinetic and Crystallographic Analyses Support a Sequential-Ordered Bi Bi Catalytic Mechanism for Escherichia Coli Glucose-1-Phosphate Thymidylyltransferase Authors: Zuccotti, S. / Zanardi, D. / Rosano, C. / Sturla, L. / Tonetti, M. / Bolognesi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h5r.cif.gz | 242.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h5r.ent.gz | 200.8 KB | Display | PDB format |
PDBx/mmJSON format | 1h5r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/1h5r ftp://data.pdbj.org/pub/pdb/validation_reports/h5/1h5r | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-GLUCOSE-1-PHOSPHATE ... , 2 types, 4 molecules ACDB
#1: Protein | Mass: 32726.465 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P37744, glucose-1-phosphate thymidylyltransferase #2: Protein | | Mass: 32705.363 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P37744, glucose-1-phosphate thymidylyltransferase |
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-Sugars , 1 types, 4 molecules
#4: Sugar | ChemComp-G1P / |
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-Non-polymers , 3 types, 486 molecules
#3: Chemical | ChemComp-THM / #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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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: 2.48 Å3/Da / Density % sol: 50.4 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.5 / Details: pH 5.50 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.3 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
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: ID14-1 / Wavelength: 0.936 |
Detector | Date: Jun 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.936 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 99207 / % possible obs: 85.4 % / Observed criterion σ(I): 3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 19.3 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 586259 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→12 Å / SU ML: 0.1297 / ESU R Free: 0.1716 / Details: PROLINE 19 IS IN CIS CONFORMATION
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Refinement step | Cycle: LAST / Resolution: 1.9→12 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 12 Å / Rfactor obs: 0.173 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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