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- PDB-2df4: Structure of tRNA-Dependent Amidotransferase GatCAB complexed wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2df4 | ||||||
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Title | Structure of tRNA-Dependent Amidotransferase GatCAB complexed with Mn2+ | ||||||
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![]() | LIGASE / MULTI PROTEIN COMPLEX | ||||||
Function / homology | ![]() asparaginyl-tRNA synthase (glutamine-hydrolyzing) activity / glutaminyl-tRNAGln biosynthesis via transamidation / glutaminyl-tRNA synthase (glutamine-hydrolysing) / glutamyl-tRNA(Gln) amidotransferase complex / Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor / glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity / regulation of translational fidelity / translation / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nakamura, A. / Yao, M. / Tanaka, I. | ||||||
![]() | ![]() Title: Ammonia channel couples glutaminase with transamidase reactions in GatCAB Authors: Nakamura, A. / Yao, M. / Chimnaronk, S. / Sakai, N. / Tanaka, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 202.1 KB | Display | ![]() |
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PDB format | ![]() | 158 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.6 KB | Display | ![]() |
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Full document | ![]() | 496.6 KB | Display | |
Data in XML | ![]() | 41.1 KB | Display | |
Data in CIF | ![]() | 55.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2dqnC ![]() 2f2aC ![]() 2g5hSC ![]() 2g5iC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 52858.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P63488, Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor | ||
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#2: Protein | Mass: 54794.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P64201, Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor | ||
#3: Protein | Mass: 11279.481 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P68807, Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 Details: 25% PEG MME 550, 0.005M magnesium chloride, 0.05M HEPES-Na , pH 7.0, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 6, 2005 |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. all: 19672 / Num. obs: 19537 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 75.2 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 12 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1916 / Rsym value: 0.432 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2G5H Resolution: 3.2→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 66.05 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.31 Å
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