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Open data
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Basic information
Entry | Database: PDB / ID: 4l56 | ||||||
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Title | tRNA guanine transglycosylase H333D mutant apo structure | ||||||
![]() | Queuine tRNA-ribosyltransferase![]() | ||||||
![]() | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() tRNA-guanosine34 preQ1 transglycosylase / tRNA wobble guanine modification / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / queuosine biosynthetic process / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nguyen, T.X.P. / Heine, A. / Klebe, G. | ||||||
![]() | ![]() Title: What Glues a Homodimer Together: Systematic Analysis of the Stabilizing Effect of an Aromatic Hot Spot in the Protein-Protein Interface of the tRNA-Modifying Enzyme Tgt. Authors: Jakobi, S. / Nguyen, P.T. / Debaene, F. / Cianferani, S. / Reuter, K. / Klebe, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 161.8 KB | Display | ![]() |
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PDB format | ![]() | 125.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4dy1C ![]() 4htbC ![]() 1pudS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 43030.773 Da / Num. of mol.: 1 / Mutation: H333D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 31821 / ZM4 / CP4 / Gene: tgt, ZMO0363 / Plasmid: pRP-IBA2 / Production host: ![]() ![]() ![]() References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase | ||
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#2: Chemical | ChemComp-ZN / | ||
#3: Chemical | ChemComp-GOL / ![]() #4: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.62 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100mM Tris 10% DMSO 7% PEG 8000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 17, 2012 / Details: Silicon, active surface 50 nm Rh-coated |
Radiation | Monochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.7→30 Å / Num. all: 46368 / Num. obs: 46368 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 16.9 Å2 / Rsym value: 0.068 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 2246 / Rsym value: 0.495 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1PUD Resolution: 1.7→29.391 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.31 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→29.391 Å
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Refine LS restraints |
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LS refinement shell |
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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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