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- PDB-5axk: Crystal structure of Thg1 like protein (TLP) -

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Basic information

Entry
Database: PDB / ID: 5axk
TitleCrystal structure of Thg1 like protein (TLP)
ComponentstRNA(His)-5'-guanylyltransferase (Thg1) like protein
KeywordsTRANSFERASE
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
tRNA(His)-5'-guanylyltransferase (Thg1) like protein
Similarity search - Component
Biological speciesMethanosarcina acetivorans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: tRNA(His)-5'-guanylyltransferase (Thg1) like protein
B: tRNA(His)-5'-guanylyltransferase (Thg1) like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1127
Polymers58,6512
Non-polymers4605
Water1,60389
1
A: tRNA(His)-5'-guanylyltransferase (Thg1) like protein
B: tRNA(His)-5'-guanylyltransferase (Thg1) like protein
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)118,22414
Polymers117,3034
Non-polymers92110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area13090 Å2
ΔGint-39 kcal/mol
Surface area44130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.255, 120.480, 157.392
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 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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 89 / 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: 3.97 Å3/Da / Density % sol: 69.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / 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: SPring-8 / Beamline: BL41XU / Wavelength: 0.978 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 41650 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rsym value: 0.082 / Net I/σ(I): 14.7
Reflection shellResolution: 2.29→2.43 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.8 / % possible all: 93.8

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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

3wbz


Resolution: 2.29→46.896 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2395 2963 7.11 %
Rwork0.206 --
obs0.2084 41649 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.29→46.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3760 0 30 89 3879
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093870
X-RAY DIFFRACTIONf_angle_d1.1095193
X-RAY DIFFRACTIONf_dihedral_angle_d16.6241483
X-RAY DIFFRACTIONf_chiral_restr0.043546
X-RAY DIFFRACTIONf_plane_restr0.005662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2891-2.32660.37881140.32061424X-RAY DIFFRACTION79
2.3266-2.36670.30011410.28641875X-RAY DIFFRACTION100
2.3667-2.40970.3421390.27861857X-RAY DIFFRACTION100
2.4097-2.45610.30641370.28811842X-RAY DIFFRACTION100
2.4561-2.50620.31700.25541860X-RAY DIFFRACTION100
2.5062-2.56070.26891600.25051794X-RAY DIFFRACTION100
2.5607-2.62030.31561360.23861884X-RAY DIFFRACTION100
2.6203-2.68580.27321390.24661869X-RAY DIFFRACTION100
2.6858-2.75840.24831210.24411871X-RAY DIFFRACTION100
2.7584-2.83950.24861450.24551856X-RAY DIFFRACTION100
2.8395-2.93120.27341420.23761847X-RAY DIFFRACTION100
2.9312-3.03590.29421300.23431882X-RAY DIFFRACTION100
3.0359-3.15750.25711350.24221865X-RAY DIFFRACTION100
3.1575-3.30110.29211400.22691874X-RAY DIFFRACTION100
3.3011-3.47510.21571380.21161857X-RAY DIFFRACTION100
3.4751-3.69280.26821530.20891877X-RAY DIFFRACTION99
3.6928-3.97770.20841490.19371848X-RAY DIFFRACTION99
3.9777-4.37780.20951730.18411855X-RAY DIFFRACTION99
4.3778-5.01060.21411490.16021866X-RAY DIFFRACTION98
5.0106-6.31040.2111240.17091912X-RAY DIFFRACTION99
6.3104-46.90590.19581280.17181871X-RAY DIFFRACTION92

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