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Yorodumi- PDB-1moq: ISOMERASE DOMAIN OF GLUCOSAMINE 6-PHOSPHATE SYNTHASE COMPLEXED WI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1moq | ||||||
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Title | ISOMERASE DOMAIN OF GLUCOSAMINE 6-PHOSPHATE SYNTHASE COMPLEXED WITH GLUCOSAMINE 6-PHOSPHATE | ||||||
Components | GLUCOSAMINE 6-PHOSPHATE SYNTHASE | ||||||
Keywords | GLUTAMINE AMIDOTRANSFERASE | ||||||
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 / protein N-linked glycosylation / fructose 6-phosphate metabolic process / glutamine metabolic process / carbohydrate metabolic process / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 1.57 Å | ||||||
Authors | Teplyakov, A. | ||||||
Citation | 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. #1: 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. #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 | 1moq.cif.gz | 96.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1moq.ent.gz | 71.4 KB | Display | PDB format |
PDBx/mmJSON format | 1moq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1moq_validation.pdf.gz | 821.9 KB | Display | wwPDB validaton report |
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Full document | 1moq_full_validation.pdf.gz | 826.8 KB | Display | |
Data in XML | 1moq_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 1moq_validation.cif.gz | 31.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mo/1moq ftp://data.pdbj.org/pub/pdb/validation_reports/mo/1moq | HTTPS FTP |
-Related structure data
Related structure data | 1morS S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 40357.004 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: HFR 3000 / Plasmid: PMA200 / Gene (production host): FRAGMENT "ISOMERASE DOMAIN" OF GLMS / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 References: UniProt: P17169, glutamine-fructose-6-phosphate transaminase (isomerizing) |
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#2: Sugar | ChemComp-GLP / |
-Non-polymers , 5 types, 424 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-MES / | #6: Chemical | ChemComp-MRD / ( | #7: 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 6.0 | ||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 72 % | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop / Details: Obmolova, G., (1994) J.Mol.Biol., 242, 703. | ||||||||||||||||||||||||||||||||||||
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: X11 / Wavelength: 0.905 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 14, 1997 / Details: CYLINDRICAL MIRROR |
Radiation | Monochromator: GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.905 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→30 Å / Num. obs: 95543 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 39.2 |
Reflection shell | Resolution: 1.57→1.6 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 5.7 / % possible all: 96.2 |
Reflection | *PLUS Rmerge(I) obs: 0.04 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: PDB ENTRY 1MOR Resolution: 1.57→10 Å / σ(F): 0
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Displacement parameters | Biso mean: 24.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.57→10 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.185 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |