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Open data
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Basic information
Entry | Database: PDB / ID: 2z3l | ||||||
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Title | complex structure of LF-transferase and peptide A | ||||||
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![]() | TRANSFERASE / LF-transferase | ||||||
Function / homology | ![]() lysine/arginine leucyltransferase / leucyl-tRNA--protein transferase activity / aminoacyltransferase activity / protein catabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Watanabe, K. / Toh, Y. / Tomita, K. | ||||||
![]() | ![]() Title: Protein-based peptide-bond formation by aminoacyl-tRNA protein transferase Authors: Watanabe, K. / Toh, Y. / Suto, K. / Shimizu, Y. / Oka, N. / Wada, T. / Tomita, K. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.3 KB | Display | ![]() |
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PDB format | ![]() | 80.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2z3kC ![]() 2z3mC ![]() 2z3nC ![]() 2z3oC ![]() 2z3pC ![]() 2dpsS 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: 26520.318 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0A8P1, lysine/arginine leucyltransferase #2: Protein/peptide | Mass: 655.766 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 50mM HEPES-Na, 0.7M tri-sodium tartrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 23, 2007 |
Radiation | Monochromator: si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→50 Å / Num. obs: 15680 / % possible obs: 98.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 115.7 Å2 / Rsym value: 0.038 / Net I/σ(I): 32.3 |
Reflection shell | Resolution: 2.75→2.85 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 1355 / Rsym value: 0.323 / % possible all: 89 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2DPS Resolution: 2.75→28.89 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 911644.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.7402 Å2 / ksol: 0.320058 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.75→28.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.88 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 8
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Xplor file |
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