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- PDB-1f3e: A NEW TARGET FOR SHIGELLOSIS: RATIONAL DESIGN AND CRYSTALLOGRAPHI... -

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Basic information

Entry
Database: PDB / ID: 1f3e
TitleA NEW TARGET FOR SHIGELLOSIS: RATIONAL DESIGN AND CRYSTALLOGRAPHIC STUDIES OF INHIBITORS OF TRNA-GUANINE TRANSGLYCOSYLASE
ComponentsQUEUINE TRNA-RIBOSYLTRANSFERASE
KeywordsTRANSFERASE / TRNA-MODIFYING ENZYME / GLYCOSYLTRANSFERASE
Function / homology
Function and homology information


tRNA-guanosine34 preQ1 transglycosylase / tRNA wobble guanine modification / tRNA-guanosine(34) queuine transglycosylase activity / : / tRNA queuosine(34) biosynthetic process / metal ion binding / cytosol
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
3,5-DIAMINOPHTHALHYDRAZIDE / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.85 Å
AuthorsGraedler, U. / Gerber, H.-D. / Goodenough-Lashua, D.M. / Garcia, G.A.G. / Ficner, R. / Reuter, K. / Stubbs, M.T. / Klebe, G.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: A new target for shigellosis: rational design and crystallographic studies of inhibitors of tRNA-guanine transglycosylase.
Authors: Gradler, U. / Gerber, H.D. / Goodenough-Lashua, D.M. / Garcia, G.A. / Ficner, R. / Reuter, K. / Stubbs, M.T. / Klebe, G.
History
DepositionJun 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2000Provider: 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 / Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / struct_biol / 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 1.4Feb 7, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: QUEUINE TRNA-RIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1833
Polymers42,9261
Non-polymers2582
Water7,530418
1
A: QUEUINE TRNA-RIBOSYLTRANSFERASE
hetero molecules

A: QUEUINE TRNA-RIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3676
Polymers85,8512
Non-polymers5154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4120 Å2
ΔGint-10 kcal/mol
Surface area26740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.670, 64.940, 71.050
Angle α, β, γ (deg.)90.00, 96.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein QUEUINE TRNA-RIBOSYLTRANSFERASE / TRNA-GUANINE TRANSGLYCOSYLASE


Mass: 42925.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis (bacteria) / Plasmid: PET9D / 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-DPZ / 3,5-DIAMINOPHTHALHYDRAZIDE


Mass: 192.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8N4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 49.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000, Tris, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 7.5
Details: Romier, C., (1996) Proteins Struct. Funct. Genet., 24, 516.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMHEPES1drop
22 M1dropNaCl
31 mMdithiothreitol1drop
412 mg/mlprotein1drop
5100 mMTris-HCl1reservoir
613 %PEG80001reservoir
71 mMdithiothreitol1reservoir

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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: Sep 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.85→35.5 Å / Num. all: 35090 / Observed criterion σ(I): 3
Reflection shellResolution: 1.85→35.5 Å / Rmerge(I) obs: 0.06 / Num. unique all: 35090 / % possible all: 96.3
Reflection
*PLUS
Num. obs: 35090 / % possible obs: 96.3 % / Num. measured all: 322171 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 93.4 % / Rmerge(I) obs: 0.336

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 1.85→35.5 Å / σ(F): 2 / σ(I): 0.0001 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.238 3509 RANDOM
Rwork0.195 --
all-35090 -
obs-322171 -
Refinement stepCycle: LAST / Resolution: 1.85→35.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2902 0 15 418 3335
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_d1.431
X-RAY DIFFRACTIONx_torsion_impr_deg1.092
X-RAY DIFFRACTIONx_torsion_deg21.491
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 35.5 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS

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