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- PDB-1it7: Crystal structure of archaeosine tRNA-guanine transglycosylase co... -

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Basic information

Entry
Database: PDB / ID: 1it7
TitleCrystal structure of archaeosine tRNA-guanine transglycosylase complexed with guanine
ComponentsArchaeosine tRNA-guanine transglycosylase
KeywordsTRANSFERASE / (ALPHA/BETA)8 BARREL / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


tRNA-guanine15 transglycosylase / pentosyltransferase activity / tRNA wobble guanine modification / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 2 / ArcTGT, C1 domain / tRNA-guanine(15) transglycosylase / tRNA-guanine transglycosylase, patch-forming domain C2 / tRNA-guanine(15) transglycosylase, C1 domain / ArcTGT, C1 domain superfamily / C1 domain of tRNA-guanine transglycosylase dimerisation / Patch-forming domain C2 of tRNA-guanine transglycosylase / ArcTGT, C2 domain / TGT, patch-forming C2 domain superfamily ...Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 2 / ArcTGT, C1 domain / tRNA-guanine(15) transglycosylase / tRNA-guanine transglycosylase, patch-forming domain C2 / tRNA-guanine(15) transglycosylase, C1 domain / ArcTGT, C1 domain superfamily / C1 domain of tRNA-guanine transglycosylase dimerisation / Patch-forming domain C2 of tRNA-guanine transglycosylase / ArcTGT, C2 domain / TGT, patch-forming C2 domain superfamily / PUA domain / Uncharacterised domain CHP00451 / PUA domain / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain superfamily / Queuine tRNA-ribosyltransferase-like / PUA domain profile. / : / tRNA-guanine(15) transglycosylase-like / Queuine tRNA-ribosyltransferase-like / Queuine tRNA-ribosyltransferase / PUA-like superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / TIM Barrel / Alpha-Beta Barrel / Roll / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANINE / tRNA-guanine(15) transglycosylase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsIshitani, R. / Nureki, O. / Fukai, S. / Kijimoto, T. / Nameki, N. / Watanabe, M. / Kondo, H. / Sekine, M. / Okada, N. / Nishimura, S. ...Ishitani, R. / Nureki, O. / Fukai, S. / Kijimoto, T. / Nameki, N. / Watanabe, M. / Kondo, H. / Sekine, M. / Okada, N. / Nishimura, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Crystal structure of archaeosine tRNA-guanine transglycosylase.
Authors: Ishitani, R. / Nureki, O. / Fukai, S. / Kijimoto, T. / Nameki, N. / Watanabe, M. / Kondo, H. / Sekine, M. / Okada, N. / Nishimura, S. / Yokoyama, S.
History
DepositionJan 11, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Oct 25, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _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_asym_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_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: Archaeosine tRNA-guanine transglycosylase
B: Archaeosine tRNA-guanine transglycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,7317
Polymers133,4002
Non-polymers3315
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-19 kcal/mol
Surface area41940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.201, 100.201, 364.658
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Archaeosine tRNA-guanine transglycosylase


Mass: 66700.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O58843, tRNA-guanosine34 preQ1 transglycosylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GUN / GUANINE


Mass: 151.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 3.43 Å3/Da / Density % sol: 64.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Na phosphate, K phosphate, Na acetate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Details: Ishitani, R., (2001) Acta Cryst., D57, 1659.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45PX / Wavelength: 1.02 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Feb 26, 2001 / Details: mirrors
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 567949 / Num. obs: 567949 / % possible obs: 98.4 % / Redundancy: 6.9 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Net I/σ(I): 19.6
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 3.78 / Num. unique all: 3973 / Rsym value: 0.382 / % possible all: 96.7
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 82107 / Num. measured all: 567949 / Rmerge(I) obs: 0.107
Reflection shell
*PLUS
% possible obs: 96.7 % / Num. unique obs: 3973 / Num. measured obs: 18480 / Rmerge(I) obs: 0.382

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IQ8

1iq8


Resolution: 2.3→50 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 8228 10 %RANDOM
Rwork0.229 ---
obs0.229 82093 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.4267 Å2 / ksol: 0.361641 e/Å3
Displacement parametersBiso mean: 35.7 Å2
Baniso -1Baniso -2Baniso -3
1-4.82 Å20 Å20 Å2
2--4.82 Å20 Å2
3----9.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9304 0 15 184 9503
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_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it2.012
X-RAY DIFFRACTIONc_scbond_it2.012
X-RAY DIFFRACTIONc_scangle_it3.042.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.358 1259 9.7 %
Rwork0.329 11665 -
obs--94 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3GUN.PARAMGUN.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 50 Å / Rfactor obs: 0.2291 / Rfactor Rfree: 0.2712 / Rfactor Rwork: 0.2291
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00669
X-RAY DIFFRACTIONc_angle_deg1.33
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.872
LS refinement shell
*PLUS
Rfactor Rfree: 0.358 / Rfactor Rwork: 0.329 / Rfactor obs: 0.329

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