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Yorodumi- PDB-2j6h: E. coli glucosamine-6-P synthase in complex with glucose-6P and 5... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2j6h | |||||||||
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Title | E. coli glucosamine-6-P synthase in complex with glucose-6P and 5-oxo- L-norleucine | |||||||||
Components | GLUCOSAMINE-FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE | |||||||||
Keywords | TRANSFERASE / AMMONIA CHANNELING | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | |||||||||
Authors | Mouilleron, S. / Golinelli-Pimpaneau, B. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Glutamine Binding Opens the Ammonia Channel and Activates Glucosamine-6-Phosphate Synthase. Authors: Mouilleron, S. / Badet-Denisot, M.A. / Golinelli-Pimpaneau, B. #1: Journal: Protein Sci. / Year: 2007 Title: Domain Motions of Glucosamine-6P Synthase: Comparison of the Anisotropic Displacements in the Crystals and the Catalytic Hinge-Bending Rotation. Authors: Mouilleron, S. / Golinelli-Pimpaneau, B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2j6h.cif.gz | 245.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j6h.ent.gz | 197.8 KB | Display | PDB format |
PDBx/mmJSON format | 2j6h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j6/2j6h ftp://data.pdbj.org/pub/pdb/validation_reports/j6/2j6h | HTTPS FTP |
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-Related structure data
Related structure data | 4amvC 1gdo 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.4338, -0.3288, 0.8389), Vector: |
-Components
#1: Protein | Mass: 66846.016 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PMA1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HB101 References: UniProt: P17169, glutamine-fructose-6-phosphate transaminase (isomerizing) #2: Chemical | #3: Chemical | #4: 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: 2.6 Å3/Da / Density % sol: 0.53 % |
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Crystal grow | pH: 7.2 Details: 12% PEG 8000, 0.1 M KCL, 5% GLYCEROL, 10 MM FRUCTOSE-6-PHOSPHATE., pH 7.20 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 14, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→30 Å / Num. obs: 57253 / % possible obs: 96 % / Observed criterion σ(I): 2.09 / Redundancy: 3.11 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.55 |
Reflection shell | Resolution: 2.35→2.39 Å / Redundancy: 2.09 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.09 / % possible all: 83 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1GDO AND 1MOQ Resolution: 2.35→15 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / SU B: 8.805 / SU ML: 0.197 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.361 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FOLLOWING RESIDUES HAVE MISSING ATOMS HIS B 273 CG, ND1, CD2, CE1, NE2.
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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: 24.93 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→15 Å
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Refine LS restraints |
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