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- PDB-1j2b: Crystal Structure Of Archaeosine tRNA-Guanine Transglycosylase Co... -

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Basic information

Entry
Database: PDB / ID: 1j2b
TitleCrystal Structure Of Archaeosine tRNA-Guanine Transglycosylase Complexed With lambda-form tRNA(Val)
Components
  • Archaeosine tRNA-guanine transglycosylase
  • tRNA(Val)
Keywordstransferase/RNA / transferase / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / transferase-RNA COMPLEX
Function / homology
Function and homology information


tRNA-guanine15 transglycosylase / pentosyltransferase activity / tRNA modification / RNA binding / metal ion binding
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 / Uncharacterised domain CHP00451 / PUA domain / PUA domain / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain profile. / PUA domain superfamily / Queuine tRNA-ribosyltransferase-like / tRNA-guanine(15) transglycosylase-like / Queuine tRNA-ribosyltransferase-like / Queuine tRNA-ribosyltransferase / PUA-like superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / TIM Barrel / Roll / Alpha-Beta Barrel / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / tRNA-guanine(15) transglycosylase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsIshitani, R. / Nureki, O. / Nameki, N. / Okada, N. / Nishimura, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2003
Title: Alternative Tertiary Structure of tRNA for Recognition by a Posttranscriptional Modification Enzyme
Authors: Ishitani, R. / Nureki, O. / Nameki, N. / Okada, N. / Nishimura, S. / Yokoyama, S.
History
DepositionDec 29, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 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
C: tRNA(Val)
D: tRNA(Val)
A: Archaeosine tRNA-guanine transglycosylase
B: Archaeosine tRNA-guanine transglycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,28410
Polymers183,0564
Non-polymers2286
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)230.834, 230.834, 269.255
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: RNA chain tRNA(Val)


Mass: 24827.746 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: synthetic tRNA transcript; sequence from Pyrococcus horikoshii
#2: Protein Archaeosine tRNA-guanine transglycosylase / E.C.2.4.2.29


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
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 3.95 Å3/Da / Density % sol: 68.58 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: citrate, ammonium phosphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Components of the solutions
IDNameCrystal-IDSol-ID
1citrateCitric acid11
2ammonium phosphate11
3citrateCitric acid12
4ammonium phosphate12
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16-8 mg/mlprotein1drop
2100 mMcitrate1droppH5.6
31.0 Mammmonium dihydrogen phosphate1drop
40.3 %xylitol1drop
5100 mMcitrate1reservoirpH5.6
61.0 Mammmonium dihydrogen phosphate1reservoir
7400 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 30 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 13, 2002 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. all: 334265 / Num. obs: 334265 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 40.6 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 16.7
Reflection shellResolution: 3.3→3.42 Å / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.31 / Num. unique all: 4055 / Rsym value: 0.487 / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 41049 / Num. measured all: 334265
Reflection shell
*PLUS
% possible obs: 99.8 %

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IQ8

1iq8


Resolution: 3.3→48.54 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 14348606.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.288 4151 10 %RANDOM
Rwork0.225 ---
obs0.225 41391 99.7 %-
all-41391 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 21.895 Å2 / ksol: 0.265241 e/Å3
Displacement parametersBiso mean: 88.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.73 Å221.96 Å20 Å2
2---3.73 Å20 Å2
3---7.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.86 Å0.71 Å
Refinement stepCycle: LAST / Resolution: 3.3→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9286 3162 6 41 12495
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.5
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it7.281.5
X-RAY DIFFRACTIONc_mcangle_it10.872
X-RAY DIFFRACTIONc_scbond_it10.022
X-RAY DIFFRACTIONc_scangle_it13.52.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.3→3.51 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.366 677 9.9 %
Rwork0.313 6150 -
obs--99.8 %
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
Refinement
*PLUS
Highest resolution: 3.3 Å / Lowest resolution: 50 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0119
X-RAY DIFFRACTIONc_angle_deg1.57
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.49

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