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Yorodumi- PDB-2g5i: Structure of tRNA-Dependent Amidotransferase GatCAB complexed wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2g5i | ||||||
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Title | Structure of tRNA-Dependent Amidotransferase GatCAB complexed with ADP-AlF4 | ||||||
Components |
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Keywords | LIGASE / MULTI PROTEIN COMPLEX | ||||||
Function / homology | Function and homology information 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 | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å | ||||||
Authors | Nakamura, A. / Yao, M. / Tanaka, I. | ||||||
Citation | Journal: Science / Year: 2006 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g5i.cif.gz | 197.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g5i.ent.gz | 151.5 KB | Display | PDB format |
PDBx/mmJSON format | 2g5i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2g5i_validation.pdf.gz | 772.1 KB | Display | wwPDB validaton report |
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Full document | 2g5i_full_validation.pdf.gz | 831.2 KB | Display | |
Data in XML | 2g5i_validation.xml.gz | 42.7 KB | Display | |
Data in CIF | 2g5i_validation.cif.gz | 58.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/2g5i ftp://data.pdbj.org/pub/pdb/validation_reports/g5/2g5i | HTTPS FTP |
-Related structure data
Related structure data | 2df4C 2dqnC 2f2aC 2g5hSC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 52858.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / Gene: gatA / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): B834 References: UniProt: P63488, Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor |
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-Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit ... , 2 types, 2 molecules BC
#2: Protein | Mass: 54794.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / Gene: gatB / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): B834 References: UniProt: P64201, Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor |
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#3: Protein | Mass: 11279.481 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / Gene: gatC / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): B834 References: UniProt: P68807, Ligases; Forming carbon-nitrogen bonds; Carbon-nitrogen ligases with glutamine as amido-N-donor |
-Non-polymers , 3 types, 92 molecules
#4: Chemical | ChemComp-MG / |
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#5: Chemical | ChemComp-ADP / |
#6: 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: 2.55 Å3/Da / Density % sol: 51.8 % |
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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: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 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: 3.35→50 Å / Num. all: 17830 / Num. obs: 17609 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 52.6 Å2 / Rmerge(I) obs: 0.127 / Rsym value: 0.127 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 3.35→3.47 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1549 / Rsym value: 0.276 / % possible all: 87.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2G5H Resolution: 3.35→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: 30.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.35→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.35→3.47 Å
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