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- PDB-4kgm: Bacterial tRNA(HIS) Guanylyltransferase (Thg1)-Like Protein in co... -

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Basic information

Entry
Database: PDB / ID: 4kgm
TitleBacterial tRNA(HIS) Guanylyltransferase (Thg1)-Like Protein in complex with ATP
ComponentsThg1-like uncharacterized protein
KeywordsTRANSFERASE / polymerase palm-like catalytic domain / GTP and tRNA binding
Function / homology
Function and homology information


tRNA guanylyltransferase activity / tRNA modification / GTP binding / magnesium ion binding / ATP 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
ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / tRNAHis guanylyltransferase catalytic domain-containing protein
Similarity search - Component
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.361 Å
AuthorsHyde, S.J. / Rao, B.S. / Eckenroth, B.E. / Jackman, J.E. / Doublie, S.
CitationJournal: Plos One / Year: 2013
Title: Structural Studies of a Bacterial tRNA(HIS) Guanylyltransferase (Thg1)-Like Protein, with Nucleotide in the Activation and Nucleotidyl Transfer Sites.
Authors: Hyde, S.J. / Rao, B.S. / Eckenroth, B.E. / Jackman, J.E. / Doublie, S.
History
DepositionApr 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.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_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: Thg1-like uncharacterized protein
B: Thg1-like uncharacterized protein
C: Thg1-like uncharacterized protein
D: Thg1-like uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,02124
Polymers114,0504
Non-polymers2,97120
Water8,179454
1
A: Thg1-like uncharacterized protein
B: Thg1-like uncharacterized protein
hetero molecules

A: Thg1-like uncharacterized protein
B: Thg1-like uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,02124
Polymers114,0504
Non-polymers2,97120
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area16740 Å2
ΔGint-148 kcal/mol
Surface area36950 Å2
MethodPISA
2
C: Thg1-like uncharacterized protein
D: Thg1-like uncharacterized protein
hetero molecules

C: Thg1-like uncharacterized protein
D: Thg1-like uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,02124
Polymers114,0504
Non-polymers2,97120
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_756-x+2,y,-z+3/21
Buried area16720 Å2
ΔGint-152 kcal/mol
Surface area37950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.156, 218.343, 126.056
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-458-

HOH

21B-435-

HOH

31B-468-

HOH

41C-451-

HOH

51D-466-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Thg1-like uncharacterized protein


Mass: 28512.436 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Gene: RBTH_06728 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3F0V8

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Non-polymers , 5 types, 474 molecules

#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 2.99 Å3/Da / Density % sol: 58.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 13% (w/v) polyethylene glycol 4000, 50 mM MgSO4 and 100 mM Tris(2-carboxyethyl) phosphine, pH 7 and ~1 mM ATP, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 26, 2011
RadiationMonochromator: ADJUSTABLE FOCUSING MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 56500 / Num. obs: 56361 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.35→2.45 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.361→36.7 Å / SU ML: 0.25 / σ(F): 1.34 / Phase error: 23.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2321 5679 10.12 %
Rwork0.1987 --
obs0.2021 56140 99.48 %
all-107600 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.361→36.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7266 0 176 454 7896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037611
X-RAY DIFFRACTIONf_angle_d0.7210342
X-RAY DIFFRACTIONf_dihedral_angle_d15.6162752
X-RAY DIFFRACTIONf_chiral_restr0.0481098
X-RAY DIFFRACTIONf_plane_restr0.0031308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.361-2.38780.27771490.2631502X-RAY DIFFRACTION90
2.3878-2.41590.29072060.2561626X-RAY DIFFRACTION98
2.4159-2.44540.26952010.24191648X-RAY DIFFRACTION99
2.4454-2.47630.30651900.25161639X-RAY DIFFRACTION100
2.4763-2.50890.27252030.23371665X-RAY DIFFRACTION100
2.5089-2.54330.28371950.23691677X-RAY DIFFRACTION100
2.5433-2.57960.27921880.24071641X-RAY DIFFRACTION100
2.5796-2.61810.27831630.23441699X-RAY DIFFRACTION100
2.6181-2.6590.2541800.22581713X-RAY DIFFRACTION100
2.659-2.70260.26981880.21811639X-RAY DIFFRACTION100
2.7026-2.74920.25631820.21771691X-RAY DIFFRACTION100
2.7492-2.79910.28341940.22961681X-RAY DIFFRACTION100
2.7991-2.85290.25492030.20761696X-RAY DIFFRACTION100
2.8529-2.91120.23561850.20631672X-RAY DIFFRACTION100
2.9112-2.97440.26951840.20361663X-RAY DIFFRACTION100
2.9744-3.04360.24821920.19861675X-RAY DIFFRACTION100
3.0436-3.11970.25251620.20611710X-RAY DIFFRACTION100
3.1197-3.2040.25831860.20341686X-RAY DIFFRACTION100
3.204-3.29820.24071920.20751682X-RAY DIFFRACTION100
3.2982-3.40460.25371880.19591725X-RAY DIFFRACTION100
3.4046-3.52620.2491900.21031678X-RAY DIFFRACTION100
3.5262-3.66720.21981940.19871683X-RAY DIFFRACTION100
3.6672-3.8340.23372070.18891664X-RAY DIFFRACTION100
3.834-4.03590.22351670.18671729X-RAY DIFFRACTION100
4.0359-4.28840.19921870.1711707X-RAY DIFFRACTION100
4.2884-4.61890.18611980.14731700X-RAY DIFFRACTION100
4.6189-5.08260.20232090.16561699X-RAY DIFFRACTION100
5.0826-5.81560.20212030.19021714X-RAY DIFFRACTION100
5.8156-7.31750.24711910.2141754X-RAY DIFFRACTION100
7.3175-36.70440.19642020.20561803X-RAY DIFFRACTION99

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