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- PDB-4gcx: tRNA-guanine transglycosylase Y106F, C158V, V233G mutant in compl... -

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Basic information

Entry
Database: PDB / ID: 4gcx
TitletRNA-guanine transglycosylase Y106F, C158V, V233G mutant in complex with preQ1
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / substrate specifity / bacterial TGT / tRNA / preQ1 / 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
7-DEAZA-7-AMINOMETHYL-GUANINE / Queuine tRNA-ribosyltransferase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsSchmidt, 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
DepositionJul 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Sep 13, 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)43,4777
Polymers42,8641
Non-polymers6136
Water7,152397
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,95314
Polymers85,7272
Non-polymers1,22612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5880 Å2
ΔGint-12 kcal/mol
Surface area26420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.189, 65.053, 70.616
Angle α, β, γ (deg.)90.00, 96.14, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-683-

HOH

21A-873-

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(DE3)pLysS
References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase
#2: Chemical ChemComp-PRF / 7-DEAZA-7-AMINOMETHYL-GUANINE


Mass: 179.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9N5O
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHR 312 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: 2.46 Å3/Da / Density % sol: 49.93 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris, 1mM 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: Dec 15, 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→50 Å / Num. all: 76733 / Num. obs: 76733 / % possible obs: 99 % / Redundancy: 3.1 % / Biso Wilson estimate: 10.23 Å2 / Net I/σ(I): 16.5
Reflection shellResolution: 1.42→1.44 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 3750 / % possible all: 96.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GEV

3gev
PDB Unreleased entry


Resolution: 1.42→24.732 Å / SU ML: 0.33 / Isotropic thermal model: isotropic / Cross valid method: R_free / σ(F): 1 / Phase error: 14.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1611 7398 10.09 %Random, 10 %
Rwork0.1312 ---
obs0.1342 73301 94.59 %-
all-73301 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.507 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.4947 Å2-0 Å23.7991 Å2
2--0.683 Å20 Å2
3----2.1777 Å2
Refinement stepCycle: LAST / Resolution: 1.42→24.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2843 0 38 397 3278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063109
X-RAY DIFFRACTIONf_angle_d1.1084225
X-RAY DIFFRACTIONf_dihedral_angle_d12.2651197
X-RAY DIFFRACTIONf_chiral_restr0.071444
X-RAY DIFFRACTIONf_plane_restr0.005562
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.43560.26792180.24921890X-RAY DIFFRACTION80
1.4356-1.45250.28142010.22451912X-RAY DIFFRACTION85
1.4525-1.47020.24672310.20532011X-RAY DIFFRACTION86
1.4702-1.48880.23662290.17712012X-RAY DIFFRACTION88
1.4888-1.50840.20172220.1692112X-RAY DIFFRACTION90
1.5084-1.52910.22222300.14882044X-RAY DIFFRACTION90
1.5291-1.55090.17792180.1292162X-RAY DIFFRACTION91
1.5509-1.57410.16852550.11682114X-RAY DIFFRACTION92
1.5741-1.59870.16472440.10722202X-RAY DIFFRACTION94
1.5987-1.62490.15242400.10322159X-RAY DIFFRACTION95
1.6249-1.65290.14952620.10042224X-RAY DIFFRACTION95
1.6529-1.68290.13992350.09752224X-RAY DIFFRACTION95
1.6829-1.71530.15332420.09592189X-RAY DIFFRACTION95
1.7153-1.75030.1312550.09212204X-RAY DIFFRACTION96
1.7503-1.78840.13672530.09582217X-RAY DIFFRACTION97
1.7884-1.82990.13122580.09742241X-RAY DIFFRACTION97
1.8299-1.87570.14192550.10442253X-RAY DIFFRACTION96
1.8757-1.92640.14782560.1142236X-RAY DIFFRACTION97
1.9264-1.9830.16552640.11742236X-RAY DIFFRACTION98
1.983-2.0470.15762850.11662284X-RAY DIFFRACTION99
2.047-2.12010.14822790.12342271X-RAY DIFFRACTION99
2.1201-2.2050.15882440.12112318X-RAY DIFFRACTION100
2.205-2.30530.14752300.12022324X-RAY DIFFRACTION99
2.3053-2.42670.14862670.1192307X-RAY DIFFRACTION99
2.4267-2.57860.15772570.12832288X-RAY DIFFRACTION99
2.5786-2.77750.16092550.13232341X-RAY DIFFRACTION99
2.7775-3.05650.16222580.13862313X-RAY DIFFRACTION99
3.0565-3.49770.1692450.13462348X-RAY DIFFRACTION99
3.4977-4.40270.14252590.13522282X-RAY DIFFRACTION97
4.4027-24.7320.17462510.18052185X-RAY DIFFRACTION91

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