+Open data
-Basic information
Entry | Database: PDB / ID: 1mp5 | ||||||
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Title | Y177F VARIANT OF S. ENTERICA RmlA | ||||||
Components | Y177F VARIANT OF S. ENTERICA RmlA BOUND TO UDP-GLUCOSE | ||||||
Keywords | TRANSFERASE | ||||||
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 / nucleotide binding / magnesium ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | Salmonella enterica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Barton, W.A. / Biggins, J.B. / Jiang, J. / Thorson, J.S. / Nikolov, D.B. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 Title: Expanding pyrimidine diphosphosugar libraries via structure-based nucleotidylyltransferase engineering Authors: Barton, W.A. / Biggins, J.B. / Jiang, J. / Thorson, J.S. / Nikolov, D.B. | ||||||
History |
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Remark 999 | SEQUENCE Author states the sequence of the deposited model differs from the published sequence, ...SEQUENCE Author states the sequence of the deposited model differs from the published sequence, because there are confirmed natural mutations in the variant of Salmonella used in this entry. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mp5.cif.gz | 228.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mp5.ent.gz | 187 KB | Display | PDB format |
PDBx/mmJSON format | 1mp5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mp5_validation.pdf.gz | 647.8 KB | Display | wwPDB validaton report |
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Full document | 1mp5_full_validation.pdf.gz | 692.1 KB | Display | |
Data in XML | 1mp5_validation.xml.gz | 30.3 KB | Display | |
Data in CIF | 1mp5_validation.cif.gz | 43.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mp/1mp5 ftp://data.pdbj.org/pub/pdb/validation_reports/mp/1mp5 | HTTPS FTP |
-Related structure data
Related structure data | 1mp3C 1mp4C 1iinS 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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Unit cell |
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-Components
#1: Protein | Mass: 32411.100 Da / Num. of mol.: 4 / Mutation: Y177F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica (bacteria) / Production host: Escherichia coli (E. coli) References: UniProt: Q9F7G8, UniProt: P26393*PLUS, glucose-1-phosphate thymidylyltransferase #2: Chemical | ChemComp-UPG / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.31 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0, temperature 100K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.4 / 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: NSLS / Beamline: X25 / Wavelength: 1.1395 Å |
Detector | Date: Jun 8, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1395 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 43514 / Observed criterion σ(I): 0 |
Reflection | *PLUS Highest resolution: 2.75 Å / % possible obs: 98.3 % / Redundancy: 5 % / Rmerge(I) obs: 0.061 |
-Processing
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IIN Resolution: 2.75→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh&Huber
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Refinement step | Cycle: LAST / Resolution: 2.75→50 Å
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Refinement | *PLUS Lowest resolution: 8 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.292 / Rfactor Rwork: 0.229 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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