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- PDB-4kr7: Crystal structure of a 4-thiouridine synthetase - RNA complex wit... -

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Basic information

Entry
Database: PDB / ID: 4kr7
TitleCrystal structure of a 4-thiouridine synthetase - RNA complex with bound ATP
Components
  • Probable tRNA sulfurtransferase
  • RNA (39-MER)
KeywordsTransferase/rna / tRNA modification / thiouridine / sulfurtransferase / adenylation / THUMP domain / PP-loop motif / 4-thiouridine synthesis / Transferase-rna complex
Function / homology
Function and homology information


tRNA-uracil-4 sulfurtransferase activity / tRNA uracil 4-sulfurtransferase / tRNA 4-thiouridine biosynthesis / CCA tRNA nucleotidyltransferase activity / thiazole biosynthetic process / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / tRNA binding / ATP binding / cytosol
Similarity search - Function
tRNA sulfurtransferase ThiI / Thil, AANH domain / Thiamine biosynthesis protein (ThiI) / VC0802-like - #30 / THUMP / THUMP domain / THUMP domain / THUMP domain profile. / VC0802-like / HUPs ...tRNA sulfurtransferase ThiI / Thil, AANH domain / Thiamine biosynthesis protein (ThiI) / VC0802-like - #30 / THUMP / THUMP domain / THUMP domain / THUMP domain profile. / VC0802-like / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / Probable tRNA sulfurtransferase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.421 Å
AuthorsNeumann, P. / Ficner, R. / Lakomek, K.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Crystal structure of a 4-thiouridine synthetase-RNA complex reveals specificity of tRNA U8 modification.
Authors: Neumann, P. / Lakomek, K. / Naumann, P.T. / Erwin, W.M. / Lauhon, C.T. / Ficner, R.
History
DepositionMay 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Sep 4, 2019Group: Data collection / Category: diffrn_source / reflns
Item: _diffrn_source.pdbx_synchrotron_site / _reflns.pdbx_Rsym_value
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Probable tRNA sulfurtransferase
B: Probable tRNA sulfurtransferase
M: RNA (39-MER)
X: RNA (39-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,5688
Polymers113,5054
Non-polymers1,0634
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.170, 113.220, 133.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsBiological unit is a homodimer. There is 1 biological unit in the asymmetric unit (chains A & B)

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Components

#1: Protein Probable tRNA sulfurtransferase / Sulfur carrier protein ThiS sulfurtransferase / Thiamine biosynthesis protein ThiI / tRNA 4- ...Sulfur carrier protein ThiS sulfurtransferase / Thiamine biosynthesis protein ThiI / tRNA 4-thiouridine synthase


Mass: 44193.094 Da / Num. of mol.: 2 / Mutation: E2K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / Gene: AAD36761, thiI, TM_1694 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9X220, tRNA uracil 4-sulfurtransferase
#2: RNA chain RNA (39-MER)


Mass: 12559.541 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 64.1 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 1 micro-liter of ThiI-RNA complex solution at 10 mg/ml in a buffer consisting of 150 mM ammonium sulfate, 20mM Tris/HCl pH 7.5 was mixed with 3 micro-liter of freshly prepared reservoir ...Details: 1 micro-liter of ThiI-RNA complex solution at 10 mg/ml in a buffer consisting of 150 mM ammonium sulfate, 20mM Tris/HCl pH 7.5 was mixed with 3 micro-liter of freshly prepared reservoir solution (2.0 M sodium formate, 100 mM sodium citrate, 2 mM DTT), VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.814 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 22, 2005 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.814 Å / Relative weight: 1
ReflectionResolution: 3.42→35 Å / Num. all: 21271 / Num. obs: 21271 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 76.586 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 14.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
3.42-3.520.672.54916149484.7
3.52-3.620.6872.345814157699.9
3.62-3.820.4583.69929268999.8
3.82-4.20.2496.3513888377299.8
4.2-4.390.14410.255290144599.8
4.39-4.580.11512.664424120499.7
4.58-4.770.09415.063753102699.6
4.77-140.04127.8627984775498.8
14-170.01661.2749915195
17-500.0219.3540416076.6
50

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.421→29.392 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 1.36 / σ(I): 0 / Phase error: 32.47 / Stereochemistry target values: ML
Details: Refinement was based on simulated annealing in torsion angle space and grouped B-factors.
RfactorNum. reflection% reflectionSelection details
Rfree0.2738 1058 5 %RANDOM
Rwork0.2304 ---
obs0.2326 21154 97.79 %-
all-21154 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 260.87 Å2 / Biso mean: 103.0531 Å2 / Biso min: 40.83 Å2
Refinement stepCycle: LAST / Resolution: 3.421→29.392 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6198 1662 64 0 7924
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018243
X-RAY DIFFRACTIONf_angle_d0.96811510
X-RAY DIFFRACTIONf_chiral_restr0.0621350
X-RAY DIFFRACTIONf_plane_restr0.0041164
X-RAY DIFFRACTIONf_dihedral_angle_d18.7363386
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4211-3.57660.41231200.38582264238490
3.5766-3.76480.37021320.309325112643100
3.7648-4.00010.33671330.268325252658100
4.0001-4.30810.29861330.244725432676100
4.3081-4.740.26041350.202625552690100
4.74-5.42220.26591340.211525502684100
5.4222-6.81730.30161350.23232567270299
6.8173-29.39270.20151360.18252581271795
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.90210.03571.27974.66570.98783.6315-0.36830.27480.73670.28750.28880.52440.16920.24-0.01420.58730.0133-0.02650.7037-0.03030.7217-21.471443.51777.4757
22.22261.15030.52483.130.43122.53650.1443-0.4283-0.00190.4365-0.21050.21820.38080.00910.22640.60380.06780.02610.8090.02280.5532-21.584521.40788.9659
32.2377-0.2469-0.3171.91780.7181.7256-0.318-0.0681-0.6696-0.04580.2062-0.12040.45750.26920.1850.61420.10670.15650.5002-0.03640.7202-16.3591-4.0758-13.0931
42.38520.39460.20192.5571-0.06242.0577-0.0170.31450.6991-0.83620.3896-0.5281-0.4293-0.646-0.18341.1188-0.27990.39750.9314-0.02381.0566-8.287134.0806-43.9568
52.6199-0.4742-0.03392.6879-0.81872.6478-0.34870.6154-0.0656-0.69770.32090.04630.4283-0.30220.09470.9019-0.13460.08190.89020.0030.6254-22.523117.7906-41.893
62.83050.2179-0.77822.3792-0.46353.1514-0.28910.0143-0.14410.02250.11950.40760.0551-0.37260.18570.4994-0.01370.10880.5233-0.11460.7036-42.14755.6828-16.7423
73.68520.39280.70052.2613-0.18361.1569-0.3791-0.35620.5581-0.28490.41970.86610.2805-0.0618-0.04261.078-0.14240.03561.03410.12041.0572-42.367127.64587.4265
80.5427-0.18040.09825.8860.87210.12510.37120.3642-0.05851.127-0.0397-1.88440.2418-0.301-0.34651.5949-0.22330.07681.3155-0.17811.23650.52917.5867-39.2507
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 77:162 )A77 - 162
2X-RAY DIFFRACTION2( CHAIN A AND RESID 3:76 )A3 - 76
3X-RAY DIFFRACTION3( CHAIN A AND ( RESID 163:388 OR RESID 401:402 ) )A163 - 388
4X-RAY DIFFRACTION3( CHAIN A AND ( RESID 163:388 OR RESID 401:402 ) )A401 - 402
5X-RAY DIFFRACTION4( CHAIN B AND RESID 77:162 )B77 - 162
6X-RAY DIFFRACTION5( CHAIN B AND RESID 3:76 )B3 - 76
7X-RAY DIFFRACTION6( CHAIN B AND ( RESID 163:388 OR RESID 401:402 ) )B163 - 388
8X-RAY DIFFRACTION6( CHAIN B AND ( RESID 163:388 OR RESID 401:402 ) )B401 - 402
9X-RAY DIFFRACTION7( CHAIN M AND RESID 1:39 )M1 - 39
10X-RAY DIFFRACTION8( CHAIN X AND RESID 1:39 )X1 - 39

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