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- PDB-1k4h: CRYSTAL STRUCTURE OF TRNA-GUANINE TRANSGLYCOSYLASE (TGT) COMPLEXE... -

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Basic information

Entry
Database: PDB / ID: 1k4h
TitleCRYSTAL STRUCTURE OF TRNA-GUANINE TRANSGLYCOSYLASE (TGT) COMPLEXED WITH 2,6-Diamino-8-propylsulfanylmethyl-3H-quinazoline-4-one
ComponentsTRNA-GUANINE-TRANSGLYCOSYLASE
KeywordsTRANSFERASE / TRNA-MODIFYING ENZYME / GLYCOSYLTRANSFERASE
Function / homology
Function and homology information


tRNA-guanosine34 preQ1 transglycosylase / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / queuosine biosynthetic process / metal ion binding
Similarity search - Function
Queuine tRNA-ribosyltransferase-like / : / tRNA-guanine transglycosylase / tRNA-guanine(15) transglycosylase-like / Queuine tRNA-ribosyltransferase-like / Queuine tRNA-ribosyltransferase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-APQ / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsBrenk, R. / Meyer, E.A. / Castellano, R.K. / Furler, M. / Stubbs, M.T. / Klebe, G. / Diederich, F.
CitationJournal: Chembiochem / Year: 2002
Title: De novo design, synthesis, and in vitro evaluation of inhibitors for prokaryotic tRNA-guanine transglycosylase: a dramatic sulfur effect on binding affinity.
Authors: Meyer, E.A. / Brenk, R. / Castellano, R.K. / Furler, M. / Klebe, G. / Diederich, F.
History
DepositionOct 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 19, 2020Group: Advisory / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _pdbx_struct_assembly_prop.biol_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._pdbx_struct_assembly_prop.biol_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRNA-GUANINE-TRANSGLYCOSYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2553
Polymers42,9261
Non-polymers3302
Water7,314406
1
A: TRNA-GUANINE-TRANSGLYCOSYLASE
hetero molecules

A: TRNA-GUANINE-TRANSGLYCOSYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5116
Polymers85,8512
Non-polymers6604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4520 Å2
ΔGint-15 kcal/mol
Surface area26610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.71, 64.99, 71.07
Angle α, β, γ (deg.)90.00, 96.44, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein TRNA-GUANINE-TRANSGLYCOSYLASE / TGT / QUEUINE TRNA-RIBOSYLTRANSFERASE / GUANINE INSERTION ENZYME


Mass: 42925.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-APQ / 2,6-DIAMINO-8-PROPYLSULFANYLMETHYL-3H-QUINAZOLINE-4-ONE


Mass: 264.347 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16N4OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.25 %
Crystal growTemperature: 290 K / Method: 8.5 / pH: 8.5 / Details: TRIS, PEG 8000, DMSO, pH 8.50, temperature 290K
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Details: Romier, C., (1996) Proteins: Struct.,Funct., Genet., 24, 516.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMTris-HCl1reservoir
213 %PEG80001reservoir
31 mMdithiothreitol1reservoir
40.2 %agarose1reservoir
510 mMHEPES1droppH7.5
62 M1dropNaCl
71 mMdithiothreitol1drop
812 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 5, 2001 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. obs: 38143 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.22 % / Rsym value: 0.05 / Net I/σ(I): 16.26
Reflection shellResolution: 1.8→1.86 Å / Mean I/σ(I) obs: 3.96 / Rsym value: 0.247 / % possible all: 99.6
Reflection
*PLUS
Num. measured all: 351534

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1PUD

1pud


Resolution: 1.8→40.8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.229 3814 10 %RANDOM
Rwork0.196 ---
all-38143 --
obs-37887 99.6 %-
Refinement stepCycle: LAST / Resolution: 1.8→40.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2902 0 19 406 3327
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.278
LS refinement shellResolution: 1.8→1.83 Å
RfactorNum. reflection% reflection
Rfree0.35 188 11.6 %
Rwork0.318 --
obs-1622 -
Refinement
*PLUS
Num. reflection obs: 38143 / Rfactor obs: 0.196 / Rfactor Rfree: 0.229 / Rfactor Rwork: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.35 / Rfactor Rwork: 0.318 / Rfactor obs: 0.318

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