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- PDB-4pun: tRNA-Guanine Transglycosylase (TGT) Apo-Structure pH 7.8 -

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Basic information

Entry
Database: PDB / ID: 4pun
TitletRNA-Guanine Transglycosylase (TGT) Apo-Structure pH 7.8
ComponentsQueuine tRNA-ribosyltransferase
Keywordstransferase/transferase inhibitor / Transferase / Guanine Exchange Enzyme / Guanine / preQ1 / tRNA / transferase-transferase inhibitor complex
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 subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsNeeb, M. / Heine, A. / Klebe, G.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Chasing Protons: How Isothermal Titration Calorimetry, Mutagenesis, and pKa Calculations Trace the Locus of Charge in Ligand Binding to a tRNA-Binding Enzyme.
Authors: Neeb, M. / Czodrowski, P. / Heine, A. / Barandun, L.J. / Hohn, C. / Diederich, F. / Klebe, G.
History
DepositionMar 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Sep 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_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_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)43,0693
Polymers42,9261
Non-polymers1442
Water6,720373
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1386
Polymers85,8512
Non-polymers2874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area3720 Å2
ΔGint-10 kcal/mol
Surface area26700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.500, 64.650, 69.930
Angle α, β, γ (deg.)90.00, 95.95, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-598-

HOH

21A-767-

HOH

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Components

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


Mass: 42925.703 Da / Num. of mol.: 1 / Fragment: Guanine Insertion Enzyme
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis subsp. mobilis (bacteria)
Strain: ATCC 31821 / ZM4 / CP4 / Gene: tgt, ZMO0363 / Plasmid: pET9d-ZM4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS HAVE INDICATED THAT SWISSPROT FOR P28720 HAS A MISSANNOTATION. THE CORRECT RESIDUE AT THE ...AUTHORS HAVE INDICATED THAT SWISSPROT FOR P28720 HAS A MISSANNOTATION. THE CORRECT RESIDUE AT THE POSITION IS LYS. CFR. PAPER REUTER K.K.H., FICNER R.; J. BACTERIOL. 177:5284-5288(1995).

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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: 2.37 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100 mM MES, 10% DMSO, 13% PEG 8000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97627 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2013
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97627 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. all: 107127 / Num. obs: 107127 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 14.5 Å2 / Rsym value: 0.03 / Net I/σ(I): 18
Reflection shellResolution: 1.25→1.3 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 11652 / Rsym value: 0.5 / % possible all: 95.3

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1PUD

1pud


Resolution: 1.25→45.006 Å / SU ML: 0.13 / Cross valid method: R-free / σ(F): 1.35 / Phase error: 15.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1615 5357 5 %Random
Rwork0.1389 ---
obs0.14 107126 96.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.25→45.006 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2848 0 5 373 3226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123002
X-RAY DIFFRACTIONf_angle_d1.4834065
X-RAY DIFFRACTIONf_dihedral_angle_d12.9221125
X-RAY DIFFRACTIONf_chiral_restr0.09435
X-RAY DIFFRACTIONf_plane_restr0.008541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.26420.29491750.27573311X-RAY DIFFRACTION94
1.2642-1.27910.30571730.25423298X-RAY DIFFRACTION95
1.2791-1.29470.24271780.23353385X-RAY DIFFRACTION96
1.2947-1.31110.24791750.213317X-RAY DIFFRACTION96
1.3111-1.32830.24481770.19233372X-RAY DIFFRACTION96
1.3283-1.34650.20031770.18273352X-RAY DIFFRACTION96
1.3465-1.36570.20471750.17253332X-RAY DIFFRACTION96
1.3657-1.38610.22091780.16513383X-RAY DIFFRACTION96
1.3861-1.40780.20141780.15433374X-RAY DIFFRACTION97
1.4078-1.43090.20871770.14223362X-RAY DIFFRACTION96
1.4309-1.45560.15761760.13273357X-RAY DIFFRACTION96
1.4556-1.4820.16071780.12443374X-RAY DIFFRACTION97
1.482-1.51050.17261800.11523422X-RAY DIFFRACTION98
1.5105-1.54140.13431800.10923417X-RAY DIFFRACTION98
1.5414-1.57490.13021790.10853413X-RAY DIFFRACTION98
1.5749-1.61150.14411790.10613401X-RAY DIFFRACTION98
1.6115-1.65180.14051810.1063428X-RAY DIFFRACTION98
1.6518-1.69650.14381800.10943422X-RAY DIFFRACTION98
1.6965-1.74640.15221810.11663438X-RAY DIFFRACTION98
1.7464-1.80280.14081790.11273395X-RAY DIFFRACTION98
1.8028-1.86720.1331800.11453426X-RAY DIFFRACTION98
1.8672-1.9420.13421820.11513453X-RAY DIFFRACTION98
1.942-2.03040.1411800.11883422X-RAY DIFFRACTION98
2.0304-2.13740.15541810.12823450X-RAY DIFFRACTION98
2.1374-2.27130.14871780.13143369X-RAY DIFFRACTION97
2.2713-2.44670.15251790.13443405X-RAY DIFFRACTION97
2.4467-2.69290.17071770.14623361X-RAY DIFFRACTION96
2.6929-3.08240.16361790.15113407X-RAY DIFFRACTION96
3.0824-3.88320.15431790.14363408X-RAY DIFFRACTION96
3.8832-45.03510.16881860.15153515X-RAY DIFFRACTION97

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