+Open data
-Basic information
Entry | Database: PDB / ID: 1gz5 | ||||||
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Title | Trehalose-6-phosphate synthase. OtsA | ||||||
Components | ALPHA-TREHALOSE-PHOSPHATE SYNTHASE | ||||||
Keywords | SYNTHASE / TREHALOSE / GLYCOSYLTRANSFERASE / ROSSMANN-FOLD / GLUCOSE-6-PHOSPHATE / TREHALOSE-6-PHOSPHATE | ||||||
Function / homology | Function and homology information trehalose metabolism in response to cold stress / alpha,alpha-trehalose-phosphate synthase (UDP-forming) / alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity / trehalose biosynthetic process / response to osmotic stress / DNA damage response Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.43 Å | ||||||
Authors | Gibson, R.P. / Turkenburg, J.P. / Davies, G.J. | ||||||
Citation | Journal: Chem.Biol. / Year: 2002 Title: Insights Into Trehalose Synthesis Provided by the Structure of the Retaining Glycosyltransferase Otsa Authors: Gibson, R.P. / Turkenburg, J.P. / Charnock, S.J. / Lloyd, R. / Davies, G.J. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Characterization of Escherichia Coli Otsa, a Trehalose-6-Phosphate Synthase from Glycosyltransferase Family 20 Authors: Gibson, R.P. / Lloyd, R.M. / Charnock, S.J. / Davies, G.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gz5.cif.gz | 362.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gz5.ent.gz | 300.1 KB | Display | PDB format |
PDBx/mmJSON format | 1gz5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/1gz5 ftp://data.pdbj.org/pub/pdb/validation_reports/gz/1gz5 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 51871.273 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: W3110 / Description: C-TERMINAL HIS-TAG FUSION / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): B834 References: UniProt: P31677, alpha,alpha-trehalose-phosphate synthase (UDP-forming) #2: Chemical | ChemComp-UDP / #3: Sugar | ChemComp-G6P / #4: Chemical | ChemComp-IMD / #5: 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: 2.7 Å3/Da / Density % sol: 53.3 % Description: THESE STATISTICS REFLECT SEPARATE TREATMENT OF FREIDEL MATES DURING SCALING PROCEDURE. TRUE MULTIPLICITY IS THUS APPROXIMATALY TWICE THE VALUE GIVEN | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 14% PEG4000, 0.15M NAAC, 0.1M IMIDAZOLE PH 7.5, 10MM MG-UDP, 10MM G6P | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | |||||||||||||||||||||||||||||||||||
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: ID14-4 / Wavelength: 0.9392 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9392 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→20 Å / Num. obs: 86205 / % possible obs: 99.9 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.45→2.54 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 2.4 / % possible all: 99.5 |
Reflection | *PLUS Lowest resolution: 20 Å |
Reflection shell | *PLUS % possible obs: 99.5 % / Rmerge(I) obs: 0.43 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.43→100 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.943 / SU B: 9.449 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.427 / ESU R Free: 0.242 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: TLS REFINEMENT USED THROUGHOUT. MOLECULE C SHOWS LARGE DISORDER IN ITS N-TERMINAL DOMAIN REFLECTED IN LARGE TLS VALUES AND POOR ELECTRON DENSITY. RESIDUES ALA 208 B AND ALA 208 D COULD NOT ...Details: TLS REFINEMENT USED THROUGHOUT. MOLECULE C SHOWS LARGE DISORDER IN ITS N-TERMINAL DOMAIN REFLECTED IN LARGE TLS VALUES AND POOR ELECTRON DENSITY. RESIDUES ALA 208 B AND ALA 208 D COULD NOT BE BUILT INTO THE ELECTRON DENSITY DUE TO LARGE DISORDER FOUND IN THESE LOOP REGIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.54 Å2
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Refinement step | Cycle: LAST / Resolution: 2.43→100 Å
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Refine LS restraints |
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