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- PDB-4fps: tRNA-Guanine Transglycosylase in complex with adamantyl-substitut... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4fps | ||||||
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Title | tRNA-Guanine Transglycosylase in complex with adamantyl-substituted lin-benzoguanine ligand | ||||||
![]() | Queuine tRNA-ribosyltransferase | ||||||
![]() | TRANSFERASE/TRANSFERASE inhibitor / TIM BARREL / GLYCOSYLTRANSFERASE / QUEUOSINE / BIOSYNTHESIS / TRANSFERASE / TRNA PROCESSING / TRNA / TRANSFERASE-TRANSFERASE inhibitor complex | ||||||
Function / homology | ![]() tRNA-guanosine34 preQ1 transglycosylase / tRNA wobble guanine modification / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / queuosine biosynthetic process / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Immekus, F. / Klebe, G. | ||||||
![]() | ![]() Title: Studies on TGT homodimer interface Authors: Immekus, F. / Barandun, L.J. / Betz, M. / Debaene, F. / Petiot, S. / Sanglier-Cianferani, S. / Diederich, F. / 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 | ![]() | 91.3 KB | Display | ![]() |
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PDB format | ![]() | 65.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 786.5 KB | Display | ![]() |
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Full document | ![]() | 792.2 KB | Display | |
Data in XML | ![]() | 17.7 KB | Display | |
Data in CIF | ![]() | 26.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4fr1C ![]() 4fr6C ![]() 4fsaC ![]() 1p0dS 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: 42925.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 31821 / ZM4 / CP4 / Gene: tgt, ZMO0363 / Plasmid: PET9D / Production host: ![]() ![]() References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-0UX / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 48.44 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100 MM MES, 1MM DTT, 10% DMSO, 13% PEG8000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Dec 10, 2009 / Details: Rh-coated silicon with indirect water cooling |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→30 Å / Num. all: 70951 / Num. obs: 70951 / % possible obs: 99.1 % / Redundancy: 2.8 % / Biso Wilson estimate: 14.86 Å2 / Rsym value: 0.064 / Net I/σ(I): 16.89 |
Reflection shell | Resolution: 1.45→1.48 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.09 / Num. unique all: 3478 / Rsym value: 0.461 / % possible all: 97.6 |
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Processing
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Refinement | Starting model: pdb entry 1P0D Resolution: 1.45→30 Å / Num. parameters: 12151 / Num. restraintsaints: 11502 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
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Refine analyze | Num. disordered residues: 6 / Occupancy sum hydrogen: 2629 / Occupancy sum non hydrogen: 3009 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→30 Å
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Refine LS restraints |
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