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- PDB-4h6e: tRNA-guanine transglycosylase Y106F, C158V, V233G mutant apo structure -

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Basic information

Entry
Database: PDB / ID: 4h6e
TitletRNA-guanine transglycosylase Y106F, C158V, V233G mutant apo structure
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / substrate specificity / bacterial TGT / preQ1 / tRNA / queuine / guanine exchange enzyme
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
Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsBiela, I. / Tidten-Luksch, N. / Heine, A. / Reuter, K. / Klebe, G.
CitationJournal: Plos One / Year: 2013
Title: Investigation of Specificity Determinants in Bacterial tRNA-Guanine Transglycosylase Reveals Queuine, the Substrate of Its Eucaryotic Counterpart, as Inhibitor.
Authors: Biela, I. / Tidten-Luksch, N. / Immekus, F. / Glinca, S. / Nguyen, T.X. / Gerber, H.D. / Heine, A. / Klebe, G. / Reuter, K.
History
DepositionSep 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _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: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5749
Polymers42,8641
Non-polymers7108
Water7,584421
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,14718
Polymers85,7272
Non-polymers1,42016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7030 Å2
ΔGint-21 kcal/mol
Surface area25750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.038, 64.796, 70.530
Angle α, β, γ (deg.)90.00, 96.13, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-632-

HOH

21A-656-

HOH

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Components

#1: Protein Queuine tRNA-ribosyltransferase / Guanine insertion enzyme / tRNA-guanine transglycosylase


Mass: 42863.613 Da / Num. of mol.: 1 / Mutation: Y106F, C158V, V233G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis (bacteria) / Strain: ATCC 31821 / ZM4 / CP4 / Gene: tgt, ZMO0363 / Plasmid: pET9d-ZM-Y106F_C158V_V233G / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE(3)pLysS
References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHR312 TO LYS CONFLICT IN UNP ENTRY P28720

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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: 2.41 Å3/Da / Density % sol: 49.05 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris, 1 mM DTT, 10% DMSO, 12% PEG 8000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 113.15 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 21, 2010 / Details: mirror
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.42→30 Å / Num. all: 76898 / Num. obs: 72492 / % possible obs: 96.7 % / Redundancy: 2.8 % / Biso Wilson estimate: 10.92 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 22.9
Reflection shellResolution: 1.42→1.44 Å / Redundancy: 2.1 % / Rsym value: 0.046 / % possible all: 87.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GVE

3gve


Resolution: 1.42→26.389 Å / SU ML: 0.12 / σ(F): 0.06 / Phase error: 15.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1744 2000 2.76 %
Rwork0.1484 --
obs0.1491 72492 94.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.42→26.389 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2857 0 43 421 3321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013108
X-RAY DIFFRACTIONf_angle_d1.3694203
X-RAY DIFFRACTIONf_dihedral_angle_d12.9541171
X-RAY DIFFRACTIONf_chiral_restr0.08445
X-RAY DIFFRACTIONf_plane_restr0.007558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.45560.22761250.17834415X-RAY DIFFRACTION83
1.4556-1.4950.18991400.15934923X-RAY DIFFRACTION93
1.495-1.53890.17071420.15534999X-RAY DIFFRACTION94
1.5389-1.58860.1771430.13725047X-RAY DIFFRACTION95
1.5886-1.64540.18481450.13425117X-RAY DIFFRACTION96
1.6454-1.71120.16871450.14285089X-RAY DIFFRACTION96
1.7112-1.78910.18151450.14915119X-RAY DIFFRACTION96
1.7891-1.88340.16311450.13695118X-RAY DIFFRACTION96
1.8834-2.00140.1661470.1425174X-RAY DIFFRACTION96
2.0014-2.15580.15511460.13565155X-RAY DIFFRACTION97
2.1558-2.37270.18131460.14485132X-RAY DIFFRACTION96
2.3727-2.71570.19131450.15045125X-RAY DIFFRACTION96
2.7157-3.42030.15061450.15335116X-RAY DIFFRACTION95
3.4203-26.39310.18521410.15624963X-RAY DIFFRACTION91
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7337-0.33720.3610.2844-0.02880.52380.0230.0404-0.04070.00950.00530.00170.06420.0059-0.02220.03050.0007-0.00160.023-0.00050.033414.085-1.765717.2576
21.2655-0.03620.07820.45950.49250.96870.0192-0.10840.2328-0.038-0.02590.0214-0.1209-0.11380.05020.0482-0.001-0.00210.07630.00530.0632-0.24289.637819.7895
30.50230.24930.44330.85190.80381.8447-0.13630.06160.2035-0.27280.05510.0272-0.5069-0.03280.06220.12590.0043-0.02420.03080.01010.12928.595816.23923.3215
41.5460.92730.99040.6030.96943.6966-0.18150.0650.5086-0.1519-0.0430.4189-0.5872-0.3581-0.52380.0740.0442-0.02580.0923-0.00620.16562.715118.857327.9018
50.96170.35570.32310.99770.49790.616-0.02350.01050.1361-0.02180.04730.0028-0.13720.00210.02480.05620.00420.00130.0357-0.01890.053817.360516.528231.4399
61.45360.1215-0.08381.28850.07761.05310.0208-0.04650.06320.0120.0128-0.0647-0.03970.0592-0.02460.0330.0092-0.01010.0164-0.01050.019620.69369.974429.7002
71.0827-0.15480.05470.75730.26951.26220.05920.02020.08920.00130.0411-0.1244-0.15610.1143-0.04420.0359-0.0020.01460.0472-0.01230.064328.32099.188621.1506
80.4599-0.21780.75110.0973-0.34591.1817-0.06420.04610.05260.03320.04240.0176-0.13430.00260.0830.03590.0025-0.00020.04580.01230.066919.27610.65384.7103
90.9185-0.13360.03941.0189-0.0231.07740.02690.0686-0.0149-0.096-0.0256-0.09510.0940.12110.00520.03120.00190.00530.05240.00260.039312.5156.7953-10.4298
100.4068-0.24720.38990.2923-0.18660.3844-0.00820.16610.0751-0.0292-0.0488-0.12370.05550.112-0.02540.02810.01630.00510.06110.00540.055522.37421.28324.0357
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 11:62 )A11 - 62
2X-RAY DIFFRACTION2( CHAIN A AND RESID 63:93 )A63 - 93
3X-RAY DIFFRACTION3( CHAIN A AND RESID 94:121 )A94 - 121
4X-RAY DIFFRACTION4( CHAIN A AND RESID 122:147 )A122 - 147
5X-RAY DIFFRACTION5( CHAIN A AND RESID 148:188 )A148 - 188
6X-RAY DIFFRACTION6( CHAIN A AND RESID 189:236 )A189 - 236
7X-RAY DIFFRACTION7( CHAIN A AND RESID 237:264 )A237 - 264
8X-RAY DIFFRACTION8( CHAIN A AND RESID 265:304 )A265 - 304
9X-RAY DIFFRACTION9( CHAIN A AND RESID 305:339 )A305 - 339
10X-RAY DIFFRACTION10( CHAIN A AND RESID 340:383 )A340 - 383

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