+Open data
-Basic information
Entry | Database: PDB / ID: 2g5h | ||||||
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Title | Structure of tRNA-Dependent Amidotransferase GatCAB | ||||||
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 / SAD / Resolution: 2.5 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 | 2g5h.cif.gz | 202.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g5h.ent.gz | 159.5 KB | Display | PDB format |
PDBx/mmJSON format | 2g5h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2g5h_validation.pdf.gz | 455.1 KB | Display | wwPDB validaton report |
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Full document | 2g5h_full_validation.pdf.gz | 500.3 KB | Display | |
Data in XML | 2g5h_validation.xml.gz | 41.1 KB | Display | |
Data in CIF | 2g5h_validation.cif.gz | 56.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/2g5h ftp://data.pdbj.org/pub/pdb/validation_reports/g5/2g5h | HTTPS FTP |
-Related 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: 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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#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 |
#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 |
#4: Chemical | ChemComp-MG / |
#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: 2.51 Å3/Da / Density % sol: 51.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 25% PEG MME 550, 0.005M magnesium chloride, 0.05M HEPES-Na, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 26, 2005 |
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: 2.5→50 Å / Num. all: 47908 / Num. obs: 41591 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 54.5 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 24.1 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 6 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 4.6 / Num. unique all: 4633 / Rsym value: 0.426 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→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: 60.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å
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