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Yorodumi- PDB-1ofd: Glutamate Synthase from Synechocystis sp in complex with 2-Oxoglu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ofd | ||||||
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Title | Glutamate Synthase from Synechocystis sp in complex with 2-Oxoglutarate at 2.0 Angstrom resolution | ||||||
Components | FERREDOXIN-DEPENDENT GLUTAMATE SYNTHASE 2 | ||||||
Keywords | OXIDOREDUCTASE / COMPLEX ENZYME / SUBSTRATE CHANNELING / AMIDOTRANSFERASE / FLAVOPROTEIN / IRON-SULPHUR / FD-GOGAT | ||||||
Function / homology | Function and homology information glutamate synthase (ferredoxin) / glutamate synthase (NADH) activity / glutamate synthase (ferredoxin) activity / ammonia assimilation cycle / L-glutamate biosynthetic process / glutamate biosynthetic process / 3 iron, 4 sulfur cluster binding / metal ion binding Similarity search - Function | ||||||
Biological species | SYNECHOCYSTIS SP. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Van Den heuvel, R.H.H. / Mattevi, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: The Active Conformation of Glutamate Synthase and its Binding to Ferredoxin Authors: Van Den Heuvel, R.H.H. / Svergun, D.I. / Petoukhov, M.V. / Coda, A. / Curti, B. / Ravasio, S. / Vanoni, M.A. / Mattevi, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ofd.cif.gz | 596.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ofd.ent.gz | 479.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ofd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/1ofd ftp://data.pdbj.org/pub/pdb/validation_reports/of/1ofd | HTTPS FTP |
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-Related structure data
Related structure data | 1ofeC 1offC 1llwS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.99079, -0.13529, 0.00613), Vector: |
-Components
#1: Protein | Mass: 165711.688 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNECHOCYSTIS SP. (bacteria) / Strain: PCC6803 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): CLR207 RECA References: UniProt: P55038, glutamate synthase (ferredoxin) #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | CATALYSES THE REACTION 2 L-GLUTAMATE + 2 OXIDIZED FERREDOXIN TO L-GLUTAMINE + 2-OXOGLUTARATE + 2 ...CATALYSES THE REACTION 2 L-GLUTAMATE + 2 OXIDIZED FERREDOXIN | |
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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: 2.77 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.50 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ID14-2 / Wavelength: 1 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 238970 / % possible obs: 96.5 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.068 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.256 / % possible all: 94.1 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 119.5 Å / Num. measured all: 1162167 / Rmerge(I) obs: 0.068 |
Reflection shell | *PLUS % possible obs: 94.1 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 2.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LLW Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.91 / SU B: 3.684 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: NONE
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.09 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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