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- PDB-1p0e: CRYSTAL STRUCTURE OF ZYMOMONAS MOBILIS tRNA-GUANINE TRANSGLYCOSYL... -

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Basic information

Entry
Database: PDB / ID: 1p0e
TitleCRYSTAL STRUCTURE OF ZYMOMONAS MOBILIS tRNA-GUANINE TRANSGLYCOSYLASE (TGT) COCRYSTALLISED WITH PREQ1 AT PH 5.5
ComponentsQueuine tRNA-ribosyltransferase
KeywordsTRANSFERASE / Protein-substrate complex
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 / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsBrenk, R. / Stubbs, M.T. / Heine, A. / Reuter, K. / Klebe, G.
CitationJournal: Chembiochem / Year: 2003
Title: Flexible adaptations in the structure of the tRNA-modifying enzyme tRNA-guanine transglycosylase and their implications for substrate selectivity, reaction mechanism and structure-based drug design
Authors: Brenk, R. / Stubbs, M.T. / Heine, A. / Reuter, K. / Klebe, G.
History
DepositionApr 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 19, 2020Group: Advisory / Database references / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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
Revision 1.4Aug 16, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1703
Polymers42,9261
Non-polymers2452
Water2,090116
1
A: Queuine tRNA-ribosyltransferase
hetero molecules

A: Queuine tRNA-ribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3416
Polymers85,8512
Non-polymers4894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area4150 Å2
ΔGint-7 kcal/mol
Surface area25880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.470, 91.870, 165.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 42925.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis (bacteria) / Gene: TGT / Plasmid: pET9d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
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-PRF / 7-DEAZA-7-AMINOMETHYL-GUANINE


Mass: 179.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9N5O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.96 Å3/Da / Density % sol: 58.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 8000, MES, DMSO, DTT, preQ1, pH 5.50, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Details: Romier, C., (1996) Proteins: Struct.,Funct., Genet., 24, 516.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMTris-HCl1reservoir
213 %PEG80001reservoir
31 mMdithiothreitol1reservoir
40.2 %agarose1reservoir
510 mMHEPES1droppH7.5
62 M1dropNaCl
71 mMdithiothreitol1drop
812 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 18, 2003 / Details: MIRRORS
RadiationMonochromator: YALE MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. all: 19371 / Num. obs: 19371 / % possible obs: 97.9 % / Redundancy: 4.9 % / Biso Wilson estimate: 37.9 Å2 / Rsym value: 0.096
Reflection shellResolution: 2.4→2.46 Å / Rsym value: 0.42 / % possible all: 99.5
Reflection
*PLUS
Num. measured all: 94879 / Rmerge(I) obs: 0.096
Reflection shell
*PLUS
% possible obs: 99.5 % / Rmerge(I) obs: 0.42

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1PUD

1pud


Resolution: 2.4→25 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 357438.28 / Data cutoff high rms absF: 357438.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1811 9.8 %RANDOM
Rwork0.206 ---
obs0.206 18457 93.9 %-
all-19371 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.4664 Å2 / ksol: 0.303438 e/Å3
Displacement parametersBiso mean: 40.8 Å2
Baniso -1Baniso -2Baniso -3
1-6.7 Å20 Å20 Å2
2--0.06 Å20 Å2
3----6.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2828 0 14 116 2958
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.881.5
X-RAY DIFFRACTIONc_mcangle_it2.92
X-RAY DIFFRACTIONc_scbond_it2.822
X-RAY DIFFRACTIONc_scangle_it3.722.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.31 294 10.1 %
Rwork0.283 2622 -
obs--90.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5PQ1.PARPQ1.TOP
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84

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