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- PDB-1pud: TRNA-GUANINE TRANSGLYCOSYLASE -

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Basic information

Entry
Database: PDB / ID: 1pud
TitleTRNA-GUANINE TRANSGLYCOSYLASE
ComponentsTRNA-GUANINE TRANSGLYCOSYLASE
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
Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.85 Å
AuthorsRomier, C. / Reuter, K. / Suck, D. / Ficner, R.
Citation
Journal: EMBO J. / Year: 1996
Title: Crystal structure of tRNA-guanine transglycosylase: RNA modification by base exchange.
Authors: Romier, C. / Reuter, K. / Suck, D. / Ficner, R.
#1: Journal: Proteins / Year: 1996
Title: Purification, Crystallization, and Preliminary X-Ray Diffraction Studies of tRNA-Guanine Transglycosylase from Zymomonas Mobilis
Authors: Romier, C. / Ficner, R. / Reuter, K. / Suck, D.
#2: Journal: J.Bacteriol. / Year: 1995
Title: Sequence Analysis and Overexpression of the Zymomonas Mobilis Tgt Gene Encoding tRNA-Guanine Transglycosylase: Purification and Biochemical Characterization of the Enzyme
Authors: Reuter, K. / Ficner, R.
History
DepositionJun 28, 1996Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRNA-GUANINE TRANSGLYCOSYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9912
Polymers42,9261
Non-polymers651
Water4,720262
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: TRNA-GUANINE TRANSGLYCOSYLASE
hetero molecules

A: TRNA-GUANINE TRANSGLYCOSYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9824
Polymers85,8512
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3250 Å2
ΔGint-17 kcal/mol
Surface area26940 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)92.100, 65.100, 71.900
Angle α, β, γ (deg.)90.00, 97.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein TRNA-GUANINE TRANSGLYCOSYLASE / TGT


Mass: 42925.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis (bacteria) / Gene: TGT / Plasmid: PET-9D / Gene (production host): TGT / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50 %
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

Diffraction sourceSource: SYNCHROTRON / Site: LURE / Type: LURE / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionNum. obs: 33727 / % possible obs: 93.2 % / Rmerge(I) obs: 0.029
Reflection
*PLUS
Highest resolution: 1.85 Å / Num. measured all: 82096

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
X-PLORphasing
RefinementResolution: 1.85→8 Å / σ(F): 2
RfactorNum. reflection
Rfree0.214 -
Rwork0.19 -
obs0.19 32152
Displacement parametersBiso mean: 20.7 Å2
Refinement stepCycle: LAST / Resolution: 1.85→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2902 0 1 262 3165
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.55
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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