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- PDB-5axm: Crystal structure of Thg1 like protein (TLP) with tRNA(Phe) -

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Basic information

Entry
Database: PDB / ID: 5axm
TitleCrystal structure of Thg1 like protein (TLP) with tRNA(Phe)
Components
  • RNA (75-MER)
  • tRNA(His)-5'-guanylyltransferase (Thg1) like protein
KeywordsTransferase/RNA / Transferase / Transferase-RNA complex
Function / homology
Function and homology information


tRNA guanylyltransferase activity / tRNA modification / GTP binding / magnesium ion binding
Similarity search - Function
tRNAHis guanylyltransferase Thg1 / tRNAHis guanylyltransferase catalytic domain / tRNAHis guanylyltransferase Thg1 superfamily / tRNAHis guanylyltransferase / tRNA(His) guanylyltransferase (Thg1) / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / tRNA(His)-5'-guanylyltransferase (Thg1) like protein
Similarity search - Component
Biological speciesMethanosarcina acetivorans (archaea)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsKimura, S. / Suzuki, T. / Yu, J. / Kato, K. / Yao, M.
CitationJournal: Sci Adv / Year: 2016
Title: Template-dependent nucleotide addition in the reverse (3'-5') direction by Thg1-like protein
Authors: Kimura, S. / Suzuki, T. / Chen, M. / Kato, K. / Yu, J. / Nakamura, A. / Tanaka, I. / Yao, M.
History
DepositionJul 31, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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_conn_type
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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA(His)-5'-guanylyltransferase (Thg1) like protein
B: tRNA(His)-5'-guanylyltransferase (Thg1) like protein
P: RNA (75-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,0817
Polymers82,9843
Non-polymers974
Water1,838102
1
A: tRNA(His)-5'-guanylyltransferase (Thg1) like protein
B: tRNA(His)-5'-guanylyltransferase (Thg1) like protein
P: RNA (75-MER)
hetero molecules

A: tRNA(His)-5'-guanylyltransferase (Thg1) like protein
B: tRNA(His)-5'-guanylyltransferase (Thg1) like protein
P: RNA (75-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,16214
Polymers165,9686
Non-polymers1948
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area19330 Å2
ΔGint-182 kcal/mol
Surface area59730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.258, 127.582, 143.801
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein tRNA(His)-5'-guanylyltransferase (Thg1) like protein


Mass: 29325.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina acetivorans (archaea) / Plasmid: pET26b / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A1C7D1G9*PLUS
#2: RNA chain RNA (75-MER)


Mass: 24332.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Sequence details142nd residue in the original sequence is PYL(PYRROLYSINE). This is (PYL)142W mutant. The residues ...142nd residue in the original sequence is PYL(PYRROLYSINE). This is (PYL)142W mutant. The residues 244-251 are expression tags.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 3350, tri-potassium citrate / PH range: 7.5 - 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.97319 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97319 Å / Relative weight: 1
ReflectionResolution: 2.21→50 Å / Num. obs: 35102 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rsym value: 0.09 / Net I/σ(I): 19.4
Reflection shellResolution: 2.21→2.34 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 3.2 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WBZ, 1EHZ

3wbz

1ehz


Resolution: 2.21→48.144 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2427 1763 5.02 %
Rwork0.2155 --
obs0.2169 35099 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.21→48.144 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3710 1569 4 102 5385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075551
X-RAY DIFFRACTIONf_angle_d0.7177826
X-RAY DIFFRACTIONf_dihedral_angle_d16.5482325
X-RAY DIFFRACTIONf_chiral_restr0.029904
X-RAY DIFFRACTIONf_plane_restr0.003723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.207-2.26670.3171510.28052417X-RAY DIFFRACTION97
2.2667-2.33340.30581360.23752538X-RAY DIFFRACTION100
2.3334-2.40870.25721160.24242554X-RAY DIFFRACTION100
2.4087-2.49480.3371240.23822558X-RAY DIFFRACTION100
2.4948-2.59470.29441270.23182575X-RAY DIFFRACTION100
2.5947-2.71280.25511260.22992554X-RAY DIFFRACTION100
2.7128-2.85580.27141300.23852556X-RAY DIFFRACTION100
2.8558-3.03470.25381410.22982554X-RAY DIFFRACTION100
3.0347-3.26890.27751440.2182549X-RAY DIFFRACTION100
3.2689-3.59780.23351270.20732587X-RAY DIFFRACTION100
3.5978-4.11810.19981480.19072589X-RAY DIFFRACTION100
4.1181-5.18750.22941480.18462590X-RAY DIFFRACTION100
5.1875-48.15560.21421450.21342715X-RAY DIFFRACTION99

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