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Yorodumi- PDB-1lm1: Structural studies on the synchronization of catalytic centers in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lm1 | ||||||
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Title | Structural studies on the synchronization of catalytic centers in glutamate synthase: native enzyme | ||||||
Components | Ferredoxin-dependent glutamate synthase | ||||||
Keywords | OXIDOREDUCTASE / glutamate synthase / channeling / amidotransferase | ||||||
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. PCC 6803 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | van Den Heuvel, R.H. / Ferrari, D. / Bossi, R.T. / Ravasio, S. / Curti, B. / Vanoni, M.A. / Florencio, F.J. / Mattevi, A. | ||||||
Citation | Journal: J.BIOL.CHEM. / Year: 2002 Title: Structural studies on the synchronization of catalytic centers in glutamate synthase Authors: van Den Heuvel, R.H. / Ferrari, D. / Bossi, R.T. / Ravasio, S. / Curti, B. / Vanoni, M.A. / Florencio, F.J. / Mattevi, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lm1.cif.gz | 293.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lm1.ent.gz | 231.4 KB | Display | PDB format |
PDBx/mmJSON format | 1lm1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lm/1lm1 ftp://data.pdbj.org/pub/pdb/validation_reports/lm/1lm1 | HTTPS FTP |
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-Related structure data
Related structure data | 1llwC 1llzC 1ea0S C: citing same article (ref.) 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
#1: Protein | Mass: 165711.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: pcc6803 / Production host: Escherichia coli (E. coli) References: UniProt: P55038, glutamate synthase (ferredoxin) | ||||||
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#2: Chemical | #3: Chemical | ChemComp-FMN / | #4: Chemical | ChemComp-F3S / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.57 Å3/Da / Density % sol: 73.07 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG4000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 | ||||||||||||||||||||||||||||||||||||||||||||||||
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: ID14-3 / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 3, 2001 |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→62 Å / Num. all: 76995 / Num. obs: 76995 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 3.8 |
Reflection shell | Resolution: 2.8→2.94 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 1.7 / Num. unique all: 10697 / Rsym value: 0.512 / % possible all: 96.6 |
Reflection | *PLUS Lowest resolution: 62 Å / Num. measured all: 1595358 / Rmerge(I) obs: 0.12 |
Reflection shell | *PLUS % possible obs: 96.6 % / Rmerge(I) obs: 0.455 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EA0 Resolution: 2.8→129.1 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.891 / SU B: 15.102 / SU ML: 0.285 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.424 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 35.074 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→129.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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Refinement | *PLUS Rfactor Rfree: 0.287 / Rfactor Rwork: 0.236 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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