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Yorodumi- PDB-2v4m: The isomerase domain of human glutamine-fructose-6-phosphate tran... -
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-Basic information
Entry | Database: PDB / ID: 2v4m | ||||||
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Title | The isomerase domain of human glutamine-fructose-6-phosphate transaminase 1 (GFPT1) in complex with fructose 6-phosphate | ||||||
Components | GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMERIZING] 1 | ||||||
Keywords | TRANSFERASE / PHOSPHOPROTEIN / AMINOTRANSFERASE / FRUCTOSE 6-PHOSPHATE / ALTERNATIVE SPLICING / GLUTAMINE AMIDOTRANSFERASE / DIMER / ISOMERASE / SIS DOMAINS | ||||||
Function / homology | Function and homology information Defective GFPT1 causes CMSTA1 / Synthesis of UDP-N-acetyl-glucosamine / glutamine-fructose-6-phosphate transaminase (isomerizing) / glutamine-fructose-6-phosphate transaminase (isomerizing) activity / UDP-N-acetylglucosamine metabolic process / UDP-N-acetylglucosamine biosynthetic process / XBP1(S) activates chaperone genes / energy reserve metabolic process / carbohydrate derivative binding / fructose 6-phosphate metabolic process ...Defective GFPT1 causes CMSTA1 / Synthesis of UDP-N-acetyl-glucosamine / glutamine-fructose-6-phosphate transaminase (isomerizing) / glutamine-fructose-6-phosphate transaminase (isomerizing) activity / UDP-N-acetylglucosamine metabolic process / UDP-N-acetylglucosamine biosynthetic process / XBP1(S) activates chaperone genes / energy reserve metabolic process / carbohydrate derivative binding / fructose 6-phosphate metabolic process / protein N-linked glycosylation / glutamine metabolic process / circadian regulation of gene expression / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å | ||||||
Authors | Moche, M. / Lehtio, L. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. ...Moche, M. / Lehtio, L. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Nilsson, M.E. / Nyman, T. / Persson, C. / Sagemark, J. / Svensson, S. / Schueler, H. / Thorsell, A.G. / Tresaugues, L. / Uppenberg, J. / Van Den Berg, S. / Welin, M. / Wisniewska, M. / Weigelt, J. / Nordlund, P. / Wikstrom, M. | ||||||
Citation | Journal: To be Published Title: The Isomerase Domain of Human Gfpt1 in Complex with Fructose 6-Phosphate Authors: Moche, M. / Lehtio, L. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / ...Authors: Moche, M. / Lehtio, L. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Nilsson, M.E. / Nyman, T. / Persson, C. / Sagemark, J. / Svensson, S. / Schueler, H. / Thorsell, A.G. / Tresaugues, L. / Uppenberg, J. / Van Den Berg, S. / Welin, M. / Wisniewska, M. / Weigelt, J. / Nordlund, P. / Wikstrom, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v4m.cif.gz | 280.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v4m.ent.gz | 228.3 KB | Display | PDB format |
PDBx/mmJSON format | 2v4m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/2v4m ftp://data.pdbj.org/pub/pdb/validation_reports/v4/2v4m | HTTPS FTP |
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-Related structure data
Related structure data | 1moqS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 42376.184 Da / Num. of mol.: 4 Fragment: EACH SUBUNIT HAS TWO SIS DOMAINS, RESIDUES 332-699 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: Q06210, glutamine-fructose-6-phosphate transaminase (isomerizing) #2: Chemical | ChemComp-F6R / #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | Sequence details | C, D AND A, B ARE TWO DIMERS IN THE ASYMMETRIC UNIT. WE WORKED ON C-TERMINAL ISOMERASE DOMAIN OF ...C, D AND A, B ARE TWO DIMERS IN THE ASYMMETRIC | |
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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: 3.05 Å3/Da / Density % sol: 59.32 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.979 | |||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 27, 2005 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.29→55 Å / Num. obs: 282618 / % possible obs: 99.2 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.6 | |||||||||||||||
Reflection shell | Resolution: 2.29→2.39 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5.1 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MOQ Resolution: 2.29→54.89 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.946 / SU B: 6.38 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY THE DATASET WAS TWINNED AS DETECTED IN PHENIX XTRIAGE. STRUCTURE REFINED USING TWO TWIN DOMAINS (-H-K, K, -L) ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY THE DATASET WAS TWINNED AS DETECTED IN PHENIX XTRIAGE. STRUCTURE REFINED USING TWO TWIN DOMAINS (-H-K, K, -L) AND A TWIN FRACTION OF 0.321 AS IMPLEMENTED IN REFMAC5.5
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.27 Å2
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Refinement step | Cycle: LAST / Resolution: 2.29→54.89 Å
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Refine LS restraints |
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