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- PDB-4kr9: Crystal structure of a 4-thiouridine synthetase - RNA complex at ... -

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Basic information

Entry
Database: PDB / ID: 4kr9
TitleCrystal structure of a 4-thiouridine synthetase - RNA complex at 3.5 Angstrom resolution
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 / tRNA-uracil-4 sulfurtransferase activity / tRNA 4-thiouridine biosynthesis / thiazole biosynthetic process / CCA tRNA nucleotidyltransferase activity / thiamine biosynthetic process / thiamine diphosphate biosynthetic process / tRNA binding / ATP binding / cytosol
Similarity search - Function
tRNA sulfurtransferase ThiI / : / Thil, AANH domain / : / : / : / Thiamine biosynthesis protein (ThiI) / ThiI ferredoxin-like domain / VC0802-like - #30 / THUMP ...tRNA sulfurtransferase ThiI / : / Thil, AANH domain / : / : / : / Thiamine biosynthesis protein (ThiI) / ThiI ferredoxin-like domain / 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
RNA / RNA (> 10) / Probable tRNA sulfurtransferase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 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 1.2Apr 15, 2020Group: Data collection / Database references
Category: diffrn_source / reflns ...diffrn_source / reflns / reflns_shell / struct_ref_seq_dif
Item: _diffrn_source.pdbx_synchrotron_site / _reflns.pdbx_Rmerge_I_obs ..._diffrn_source.pdbx_synchrotron_site / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs / _struct_ref_seq_dif.details
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)


Theoretical massNumber of molelcules
Total (without water)113,5054
Polymers113,5054
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.284, 113.551, 132.151
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111((chain A and (resid 3:11 or resid 23:26 or resid...
211((chain B and (resid 3:11 or resid 23:26 or resid...
112((chain A and (resid 79:113 or resid 114: 137 or...
212((chain B and (resid 79:113 or resid 114: 137 or...
113((chain A and (resid 165:181 or resid 182:208 or resid...
213((chain B and (resid 165:181 or resid 182:208 or resid...
114chain M and (resseq 1:8 or resseq 28:35 )
214chain X and (resseq 1:8 or resseq 28:35 )
115chain M and (resid 17:19 or resid 24:27 )
215chain X and (resid 17:19 or resid 24:27 )

NCS ensembles :
ID
1
2
3
4
5

NCS oper:
IDCodeMatrixVector
1given(-0.769961, 0.633016, -0.08031), (0.637679, 0.758829, -0.13245), (-0.022901, -0.153193, -0.987931)-53.567001, 17.242001, -30.4454
2given(-0.775609, 0.627721, -0.066317), (0.630901, 0.767627, -0.112745), (-0.019866, -0.129286, -0.991408)-52.665798, 17.9702, -31.298901
3given(-0.753898, 0.654688, -0.05497), (0.654561, 0.741284, -0.148488), (-0.056465, -0.147926, -0.987385)-52.720798, 17.237, -31.391701
4given(-0.752615, 0.292585, 0.589885), (0.202431, 0.955281, -0.215547), (-0.626572, -0.042813, -0.778187)-23.955099, 12.8911, -22.110701
5given(-0.775859, 0.102933, 0.622453), (0.129382, 0.991591, -0.002708), (-0.617498, 0.078433, -0.782652)-20.7048, 20.7383, -22.559099

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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

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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: 3.41 Å3/Da / Density % sol: 63.97 %
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 mMDTT), 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: 0.978
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 25, 2006 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.474→52.165 Å / Num. obs: 20061 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 102.57 Å2 / Rsym value: 0.089 / Net I/σ(I): 9.9
Reflection shellResolution: 3.5→3.69 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.2 / Rsym value: 0.611 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.6.1_357refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→29.75 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.48 / σ(F): 1.36 / Phase error: 26.08 / Stereochemistry target values: ML
Details: REFINEMENT WAS BASED ON SIMULATED ANNEALING IN TORSION ANGLE SPACE AND GROUPED B-FACTORS.
RfactorNum. reflection% reflection
Rfree0.269 996 4.99 %
Rwork0.23 --
obs0.232 19940 98.9 %
all-19940 -
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 127.06 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 159.22 Å2
Baniso -1Baniso -2Baniso -3
1-7.4952 Å20 Å20 Å2
2---9.1395 Å20 Å2
3---1.6444 Å2
Refinement stepCycle: LAST / Resolution: 3.5→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6198 1662 0 0 7860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098439
X-RAY DIFFRACTIONf_angle_d0.97911406
X-RAY DIFFRACTIONf_dihedral_angle_d21.1413360
X-RAY DIFFRACTIONf_chiral_restr0.11342
X-RAY DIFFRACTIONf_plane_restr0.0051162
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A488X-RAY DIFFRACTIONPOSITIONAL
12B488X-RAY DIFFRACTIONPOSITIONAL0.007
21A609X-RAY DIFFRACTIONPOSITIONAL
22B609X-RAY DIFFRACTIONPOSITIONAL0.003
31A1482X-RAY DIFFRACTIONPOSITIONAL
32B1482X-RAY DIFFRACTIONPOSITIONAL0.004
41M340X-RAY DIFFRACTIONPOSITIONAL
42X340X-RAY DIFFRACTIONPOSITIONAL0.083
51M150X-RAY DIFFRACTIONPOSITIONAL
52X150X-RAY DIFFRACTIONPOSITIONAL0.711
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.68420.33811400.30122686X-RAY DIFFRACTION100
3.6842-3.91460.30961390.27612690X-RAY DIFFRACTION100
3.9146-4.21610.29431430.25932684X-RAY DIFFRACTION100
4.2161-4.63890.22011420.21452697X-RAY DIFFRACTION100
4.6389-5.30690.26841420.19892732X-RAY DIFFRACTION100
5.3069-6.67360.25471430.21532744X-RAY DIFFRACTION100
6.6736-29.74610.23811470.20042711X-RAY DIFFRACTION94
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)
12.2060.65611.95523.4546-0.03631.9007-0.2888-0.10760.8338-0.050.43280.5137-0.13660.07720.00021.3106-0.15710.05671.3848-0.15791.5632-21.479343.67117.7948
21.3958-0.4605-0.44653.2013-0.2642.353-0.2943-0.12540.42280.32490.26460.07530.0826-0.08520.00041.2080.05190.04891.5976-0.05511.1573-21.785921.55649.0589
31.32420.0571-0.99382.22720.44520.8468-0.221-0.0755-0.33750.07470.1601-0.12120.23380.4402-0.00011.16470.11170.09361.161-0.01341.2769-16.2618-3.965-13.0678
43.72180.1705-0.51181.65780.37490.0997-0.00330.18350.2877-0.36770.56040.1162-0.2171-0.05-0.00031.7933-0.36880.36051.37540.04061.5543-8.732834.2587-43.71
53.79711.05370.83940.469-0.47692.9031-0.17840.73910.0193-0.48310.2999-0.21740.2812-0.1756-0.00021.4934-0.16860.07891.54420.0211.1522-22.595517.7615-41.8984
62.36760.7192-1.39382.0736-0.13012.7591-0.17730.121-0.0962-0.14120.18730.2743-0.1586-0.51101.0685-0.02240.08331.19730.03281.2465-42.27345.3166-16.863
72.38061.884-0.74652.6451-0.1650.283-0.0815-0.44070.6918-0.3140.22850.91870.45420.25990.00042.1135-0.15730.06231.82810.13122.1691-42.673127.64317.5285
80.50750.14750.14943.1708-1.56491.28270.11880.2792-0.2820.0878-0.0988-1.76780.2373-0.0401-0.00012.0159-0.15830.10781.9211-0.35271.79450.44818.1212-38.8393
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 )A163 - 388
4X-RAY DIFFRACTION4( CHAIN B AND RESID 77:162 )B77 - 162
5X-RAY DIFFRACTION5( CHAIN B AND RESID 3:76 )B3 - 76
6X-RAY DIFFRACTION6( CHAIN B AND RESID 163:388 )B163 - 388
7X-RAY DIFFRACTION7( CHAIN M AND RESID 1:39 )M1 - 39
8X-RAY DIFFRACTION8( CHAIN X AND RESID 1:39 )X1 - 39

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