+Open data
-Basic information
Entry | Database: PDB / ID: 1i8t | ||||||
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Title | STRUCTURE OF UDP-GALACTOPYRANOSE MUTASE FROM E.COLI | ||||||
Components | UDP-GALACTOPYRANOSE MUTASE | ||||||
Keywords | ISOMERASE / Rossmann Fold / FAD / UDP-galactopyranose / mutase / contractase | ||||||
Function / homology | Function and homology information UDP-galactopyranose mutase / UDP-galactopyranose mutase activity / lipopolysaccharide biosynthetic process / flavin adenine dinucleotide binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Sanders, D.A.R. / Staines, A.G. / McMahon, S.A. / McNeil, M.R. / Whitfield, C. / Naismith, J.H. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2001 Title: UDP-galactopyranose mutase has a novel structure and mechanism. Authors: Sanders, D.A. / Staines, A.G. / McMahon, S.A. / McNeil, M.R. / Whitfield, C. / Naismith, J.H. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Molecular Placement of Experimental Electron Density: A Case Study on UDP-Galactopyranose Mutase Authors: Sanders, D.A.R. / McMahon, S.A. / Leonard, G.L. / Naimsith, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i8t.cif.gz | 169.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i8t.ent.gz | 133.5 KB | Display | PDB format |
PDBx/mmJSON format | 1i8t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i8/1i8t ftp://data.pdbj.org/pub/pdb/validation_reports/i8/1i8t | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43025.789 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P37747, UDP-galactopyranose mutase #2: Chemical | #3: 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: 2.14 Å3/Da / Density % sol: 42.48 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: PEG 4K, 0.01 mM l-cystein, Hepe, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusionDetails: used macroseeding, Sanders, D.A.R., (2001) Acta Crystallogr., Sect.D, 57, 1415. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 Å | |||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 28, 2000 | |||||||||||||||
Radiation |
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Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.4→40 Å / Num. all: 28865 / Num. obs: 28288 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 10.9 | |||||||||||||||
Reflection shell | Resolution: 2.4→2.52 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 3.3 / % possible all: 93 | |||||||||||||||
Reflection | *PLUS Lowest resolution: 40 Å / % possible obs: 98 % | |||||||||||||||
Reflection shell | *PLUS % possible obs: 93 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.4→40 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.4→40 Å
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LS refinement shell | Resolution: 2.4→2.52 Å | ||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 40 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.185 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.4 Å |