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- PDB-5j9n: tRNA guanine Transglycosylase (TGT) in co-crystallized complex wi... -

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Basic information

Entry
Database: PDB / ID: 5j9n
TitletRNA guanine Transglycosylase (TGT) in co-crystallized complex with 2-(methylamino)-1H-benzo[d]imidazole-5-carbohydrazide
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / Benzimidazole-derivatives / shigellosis / TRANSFERASE INHIBITOR
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
2-(methylamino)-1H-benzimidazole-5-carbohydrazide / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsEhrmann, F.R. / Heine, A. / Klebe, G.
CitationJournal: To be Published
Title: Benzimidazole-based Inhibitors as a Novel Scaffold to Inhibit Z.mobilis TGT and Study Protein Flexibility and the Contributions of Active Site Residues to Binding Affinity of lin-Benzopurines.
Authors: Ehrmann, F.R. / Hohn, C. / Heine, A. / Diederich, F. / Klebe, G.
History
DepositionApr 10, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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
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)43,4736
Polymers42,9261
Non-polymers5475
Water3,729207
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,94512
Polymers85,8512
Non-polymers1,09410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4920 Å2
ΔGint-18 kcal/mol
Surface area25660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.359, 64.547, 71.273
Angle α, β, γ (deg.)90.00, 92.85, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-698-

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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4) (bacteria)
Strain: ATCC 31821 / ZM4 / CP4 / Gene: tgt, ZMO0363 / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-6H9 / 2-(methylamino)-1H-benzimidazole-5-carbohydrazide


Mass: 205.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11N5O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.4 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 13% PEG 8000,100mM MES, 1mM DTT, 10% DMSO,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.64→45.12 Å / Num. obs: 49307 / % possible obs: 97.5 % / Redundancy: 3 % / Rsym value: 0.063 / Net I/σ(I): 9.28
Reflection shellResolution: 1.64→1.74 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 2.01 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1-2155_1492)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P0D

1p0d


Resolution: 1.64→41.681 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.45
RfactorNum. reflection% reflection
Rfree0.2368 2463 5 %
Rwork0.2133 --
obs0.2145 49285 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.64→41.681 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2764 0 34 207 3005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062924
X-RAY DIFFRACTIONf_angle_d0.833945
X-RAY DIFFRACTIONf_dihedral_angle_d16.4091756
X-RAY DIFFRACTIONf_chiral_restr0.05414
X-RAY DIFFRACTIONf_plane_restr0.006540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6364-1.66790.31521210.282299X-RAY DIFFRACTION87
1.6679-1.70190.28981390.2522644X-RAY DIFFRACTION99
1.7019-1.73890.25671400.22982658X-RAY DIFFRACTION99
1.7389-1.77940.25771390.21872631X-RAY DIFFRACTION100
1.7794-1.82390.25911380.2162616X-RAY DIFFRACTION100
1.8239-1.87320.241400.21842668X-RAY DIFFRACTION100
1.8732-1.92830.28121400.22642657X-RAY DIFFRACTION99
1.9283-1.99060.23261380.21542629X-RAY DIFFRACTION99
1.9906-2.06170.24541390.21352627X-RAY DIFFRACTION98
2.0617-2.14420.25271370.21332600X-RAY DIFFRACTION98
2.1442-2.24180.25491370.22762622X-RAY DIFFRACTION99
2.2418-2.360.27031370.22482609X-RAY DIFFRACTION98
2.36-2.50790.23721380.2182620X-RAY DIFFRACTION98
2.5079-2.70150.23441360.22132590X-RAY DIFFRACTION97
2.7015-2.97330.25511330.22572536X-RAY DIFFRACTION95
2.9733-3.40330.22251370.21692597X-RAY DIFFRACTION96
3.4033-4.28710.21571360.19222598X-RAY DIFFRACTION97
4.2871-41.69440.21511380.19862621X-RAY DIFFRACTION95
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)
10.5897-0.14180.39880.138-0.030.3104-0.0509-0.21570.06570.11840.0523-0.00140.0773-0.08630.00350.14940.01380.01310.1171-0.01560.10798.9074.22317.99
20.31540.2074-0.10340.1371-0.06910.0717-0.2545-0.07420.40330.02390.07050.0895-0.2591-0.37480.03140.47140.1241-0.11810.3871-0.17420.48616.757725.973226.8528
30.223-0.04230.22020.0206-0.02120.2395-0.1589-0.39490.23450.23220.1672-0.1168-0.0549-0.13840.02790.30130.07240.00970.3515-0.07730.19167.104713.441929.5076
41.1674-0.3539-0.43581.15120.25360.6204-0.0722-0.36930.30660.21850.1429-0.17540.01890.08730.00920.21790.0159-0.05760.2564-0.09430.238421.186212.602224.9508
50.5193-0.14680.57070.2586-0.12120.59870.02230.19980.073-0.1035-0.0224-0.10470.04280.194700.13610.00340.02490.18410.00810.180617.91476.8242-2.5948
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 11:105)
2X-RAY DIFFRACTION2(chain A and resid 106:135)
3X-RAY DIFFRACTION3(chain A and resid 136:159)
4X-RAY DIFFRACTION4(chain A and resid 160:289)
5X-RAY DIFFRACTION5(chain A and resid 290:382)

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