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Yorodumi- PDB-1mos: ISOMERASE DOMAIN OF GLUCOSAMINE 6-PHOSPHATE SYNTHASE COMPLEXED WI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mos | ||||||
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Title | ISOMERASE DOMAIN OF GLUCOSAMINE 6-PHOSPHATE SYNTHASE COMPLEXED WITH 2-AMINO-2-DEOXYGLUCITOL 6-PHOSPHATE | ||||||
Components | GLUCOSAMINE 6-PHOSPHATE SYNTHASE | ||||||
Keywords | TRANSFERASE / GLUTAMINE AMIDOTRANSFERASE / AMINOTRANSFERASE | ||||||
Function / homology | Function and homology information glutamine-fructose-6-phosphate transaminase (isomerizing) / glutamine-fructose-6-phosphate transaminase (isomerizing) activity / UDP-N-acetylglucosamine metabolic process / UDP-N-acetylglucosamine biosynthetic process / carbohydrate derivative binding / fructose 6-phosphate metabolic process / protein N-linked glycosylation / glutamine metabolic process / carbohydrate metabolic process / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 2 Å | ||||||
Authors | Teplyakov, A. / Obmolova, G. / Badet-Denisot, M.A. / Badet, B. | ||||||
Citation | Journal: Protein Sci. / Year: 1999 Title: The mechanism of sugar phosphate isomerization by glucosamine 6-phosphate synthase. Authors: Teplyakov, A. / Obmolova, G. / Badet-Denisot, M.A. / Badet, B. #1: Journal: Structure / Year: 1998 Title: Involvement of the C Terminus in Intramolecular Nitrogen Channeling in Glucosamine 6-Phosphate Synthase: Evidence from a 1.6 A Crystal Structure of the Isomerase Domain Authors: Teplyakov, A. / Obmolova, G. / Badet-Denisot, M.A. / Badet, B. / Polikarpov, I. #2: Journal: Structure / Year: 1997 Title: Erratum. Substrate Binding is Required for Assembly of the Active Conformation of the Catalytic Site in Ntn Amidotransferases: Evidence from the 1.8 A Crystal Structure of the Glutaminase ...Title: Erratum. Substrate Binding is Required for Assembly of the Active Conformation of the Catalytic Site in Ntn Amidotransferases: Evidence from the 1.8 A Crystal Structure of the Glutaminase Domain of Glucosamine 6-Phosphate Synthase Authors: Isupov, M.N. / Obmolova, G. / Butterworth, S. / Badet-Denisot, M.A. / Badet, B. / Polikarpov, I. / Littlechild, J.A. / Teplyakov, A. #3: Journal: Structure / Year: 1996 Title: Substrate Binding is Required for Assembly of the Active Conformation of the Catalytic Site in Ntn Amidotransferases: Evidence from the 1.8 A Crystal Structure of the Glutaminase Domain of ...Title: Substrate Binding is Required for Assembly of the Active Conformation of the Catalytic Site in Ntn Amidotransferases: Evidence from the 1.8 A Crystal Structure of the Glutaminase Domain of Glucosamine 6-Phosphate Synthase Authors: Isupov, M.N. / Obmolova, G. / Butterworth, S. / Badet-Denisot, M.A. / Badet, B. / Polikarpov, I. / Littlechild, J.A. / Teplyakov, A. #4: Journal: J.Mol.Biol. / Year: 1994 Title: Crystallization and Preliminary X-Ray Analysis of the Two Domains of Glucosamine-6-Phosphate Synthase from Escherichia Coli Authors: Obmolova, G. / Badet-Denisot, M.A. / Badet, B. / Teplyakov, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mos.cif.gz | 84.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mos.ent.gz | 67.1 KB | Display | PDB format |
PDBx/mmJSON format | 1mos.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mo/1mos ftp://data.pdbj.org/pub/pdb/validation_reports/mo/1mos | HTTPS FTP |
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-Related structure data
Related structure data | 1morC 1moqS 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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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 40357.004 Da / Num. of mol.: 1 / Fragment: ISOMERASE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: 3000HFR / Plasmid: PMA200 / Gene (production host): GLMS / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 References: UniProt: P17169, glutamine-fructose-6-phosphate transaminase (isomerizing) |
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-Non-polymers , 5 types, 186 molecules
#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-AGP / | #5: Chemical | ChemComp-MES / | #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: 4.3 Å3/Da / Density % sol: 71 % | |||||||||||||||||||||||||
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Crystal grow | pH: 6 / Details: pH 6.00 | |||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 72 % | |||||||||||||||||||||||||
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: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.84 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 8, 1997 / Details: MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.84 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. obs: 45840 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 3.6 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 3.6 / % possible all: 95.7 |
Reflection | *PLUS Num. obs: 45848 |
Reflection shell | *PLUS % possible obs: 95.7 % |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: 1MOQ Resolution: 2→12 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 37 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→12 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 15 Å / Rfactor obs: 0.248 / Rfactor Rfree: 0.286 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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