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- PDB-4pul: tRNA-Guanine Transglycosylase (TGT) Mutant D102N in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 4pul
TitletRNA-Guanine Transglycosylase (TGT) Mutant D102N in Complex with 6-Amino-2-(methylamino)-1H,7H,8H-imidazo[4,5-g]quinazolin-8-one
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
Chem-2WU / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.654 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_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)43,3124
Polymers42,9251
Non-polymers3883
Water4,702261
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,6258
Polymers85,8492
Non-polymers7756
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area3740 Å2
ΔGint-16 kcal/mol
Surface area24680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.670, 64.180, 70.360
Angle α, β, γ (deg.)90.00, 92.86, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-616-

HOH

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Components

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


Mass: 42924.719 Da / Num. of mol.: 1 / Mutation: D102N
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-D102N / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-2WU / 6-amino-2-(methylamino)-3,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one


Mass: 230.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10N6O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.36 Å3/Da / Density % sol: 47.78 %
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: 1.23953 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2012
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23953 Å / Relative weight: 1
ReflectionResolution: 1.65→80 Å / Num. all: 43729 / Num. obs: 43729 / % possible obs: 91.6 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 22.4 Å2 / Rsym value: 0.029 / Net I/σ(I): 22.3
Reflection shellResolution: 1.65→1.85 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 9984 / Rsym value: 0.275 / % possible all: 73.8

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1PUD

1pud


Resolution: 1.654→70.272 Å / SU ML: 0.17 / Cross valid method: R-free / σ(F): 1.99 / Phase error: 21.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.189 1312 3 %Random
Rwork0.1667 ---
obs0.1674 43719 91.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.654→70.272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2784 0 24 261 3069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072924
X-RAY DIFFRACTIONf_angle_d1.0563965
X-RAY DIFFRACTIONf_dihedral_angle_d12.7651087
X-RAY DIFFRACTIONf_chiral_restr0.072424
X-RAY DIFFRACTIONf_plane_restr0.005549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6542-1.72050.3189710.26992319X-RAY DIFFRACTION45
1.7205-1.79880.25691400.22054499X-RAY DIFFRACTION89
1.7988-1.89360.22891570.20515093X-RAY DIFFRACTION99
1.8936-2.01230.23671560.18965025X-RAY DIFFRACTION99
2.0123-2.16760.20011580.16295105X-RAY DIFFRACTION99
2.1676-2.38580.22021550.16255021X-RAY DIFFRACTION98
2.3858-2.7310.19421570.15885092X-RAY DIFFRACTION99
2.731-3.44080.17571590.15455113X-RAY DIFFRACTION99
3.4408-70.33590.15971590.16045140X-RAY DIFFRACTION98
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)
13.8982-0.82680.93020.6427-0.35172.3013-0.0262-0.0505-0.11690.11940.0349-0.0237-0.01180.05410.0010.14470.00730.00540.068-0.01030.1411103.37280.493716.6387
22.359-1.7456-1.6293.14321.49032.92720.0686-0.08620.42150.1360.0952-0.2603-0.2678-0.1531-0.17230.18740.0215-0.00680.16550.00520.166289.525711.037919.9174
31.85730.1167-0.12580.95690.41061.52880.0145-0.21530.2610.0950.0401-0.1232-0.27880.1222-0.04590.22330.0072-0.02410.1541-0.01870.1852107.177914.758126.8812
41.3646-0.73941.95510.6602-1.32593.1374-0.04230.11860.0398-0.0041-0.0184-0.0907-0.10310.15850.06710.154-0.0220.01650.1536-0.01570.169107.41047.6974-0.7992
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 62 )
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 93 )
3X-RAY DIFFRACTION3chain 'A' and (resid 94 through 274 )
4X-RAY DIFFRACTION4chain 'A' and (resid 275 through 383 )

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