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- PDB-4kr6: Crystal structure of a 4-thiouridine synthetase - RNA complex -

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Basic information

Entry
Database: PDB / ID: 4kr6
TitleCrystal structure of a 4-thiouridine synthetase - RNA complex
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: 2.85 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: reflns / Item: _reflns.pdbx_Rsym_value
Revision 1.3Sep 20, 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 / 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
C: RNA (39-MER)
D: RNA (39-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,3088
Polymers113,5054
Non-polymers8024
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.652, 110.325, 119.313
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

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111((chain A and (resid 4:10 or resid 24:45 or resid...
211((chain B and (resid 4:10 or resid 24:45 or resid...
112((chain A and (resid 76:109 or resid 114: 137 or...
212((chain B and (resid 76:109 or resid 114: 137 or...
113((chain A and (resid 167:181 or resid 182:209 or resid...
213((chain B and (resid 167:181 or resid 182:209 or resid...

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(0.44197, -0.804303, 0.39719), (-0.807845, -0.549359, -0.213519), (0.389934, -0.226499, -0.892552)5.71677, 21.3955, 22.489401
2given(0.499903, -0.797086, 0.338749), (-0.804237, -0.572374, -0.159973), (0.321403, -0.192464, -0.927177)8.28537, 19.502899, 22.904499
3given(0.567138, -0.741477, 0.358561), (-0.74488, -0.647521, -0.160842), (0.351436, -0.175866, -0.919545)4.09714, 19.6703, 23.623301

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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-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Hg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.92 Å3/Da / Density % sol: 57.85 %
Crystal growTemperature: 292 K / 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: BESSY / Beamline: 14.1 / Wavelength: 1.0085
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 22, 2006 / Details: MIRRORS
RadiationMonochromator: GRAPHITE, / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0085 Å / Relative weight: 1
ReflectionResolution: 2.85→30 Å / Num. obs: 30547 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 60.02 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 16.42
Reflection shellResolution: 2.85→2.95 Å / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 2.06 / % possible all: 81.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C5S

2c5s


Resolution: 2.85→30 Å / Occupancy max: 1 / Occupancy min: 0.36 / SU ML: 0.26 / σ(F): 1.99 / Phase error: 21.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.228 1513 4.98 %
Rwork0.186 --
obs0.188 30363 95.9 %
all-30363 -
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.33 Å2
Refinement stepCycle: LAST / Resolution: 2.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6232 1666 4 75 7977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128212
X-RAY DIFFRACTIONf_angle_d0.92711453
X-RAY DIFFRACTIONf_dihedral_angle_d16.9173374
X-RAY DIFFRACTIONf_chiral_restr0.0621346
X-RAY DIFFRACTIONf_plane_restr0.0041168
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A438X-RAY DIFFRACTIONPOSITIONAL
12B438X-RAY DIFFRACTIONPOSITIONAL0.323
21A580X-RAY DIFFRACTIONPOSITIONAL
22B580X-RAY DIFFRACTIONPOSITIONAL0.354
31A1484X-RAY DIFFRACTIONPOSITIONAL
32B1484X-RAY DIFFRACTIONPOSITIONAL0.316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.9420.3153990.27362024X-RAY DIFFRACTION75
2.942-3.04710.27971400.2662593X-RAY DIFFRACTION96
3.0471-3.1690.29841400.23142647X-RAY DIFFRACTION99
3.169-3.31320.2791430.21482700X-RAY DIFFRACTION99
3.3132-3.48770.22431380.20462659X-RAY DIFFRACTION99
3.4877-3.7060.24731410.17932677X-RAY DIFFRACTION98
3.706-3.99190.20271410.16682675X-RAY DIFFRACTION98
3.9919-4.3930.17671400.15132693X-RAY DIFFRACTION98
4.393-5.02740.17941430.14862699X-RAY DIFFRACTION98
5.0274-6.32890.24151420.18062698X-RAY DIFFRACTION98
6.3289-37.18150.23851460.19372785X-RAY DIFFRACTION96
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)
13.2494-1.5548-0.0413.62740.89283.2356-0.1325-0.3547-0.19980.31980.22310.50250.0286-0.47260.09660.35340.09920.02860.50060.04630.38051.474421.189-13.223
22.1924-0.1931.07352.6576-0.80373.12140.00730.18730.0903-0.0684-0.1461-0.05980.1090.36590.14390.39990.0475-0.05380.4075-0.00240.368515.38616.6487-11.7529
31.3522-0.27380.43832.1259-0.70672.1487-0-0.0235-0.266-0.07970.02450.20810.2509-0.1515-0.03340.1986-0.0303-0.00060.24970.00290.315522.0402-14.515315.0414
42.9078-1.43730.53483.26010.7073.50650.25180.5395-0.2935-0.346-0.26260.2850.0916-0.11730.06380.39280.0450.00080.5365-0.10060.5639-16.332511.236730.8838
53.8960.57240.54553.58910.97932.9550.1037-0.61850.04050.1192-0.10730.262-0.07610.0990.05560.42970.05910.0320.4850.01430.32883.95327.836538.0575
62.99020.0306-0.34392.23810.50512.8262-0.018-0.05120.258-0.1026-0.0218-0.1855-0.54870.38190.0170.2977-0.072-0.02230.21020.02760.237732.530810.27619.8653
72.776-1.43710.21473.08250.31751.34850.55310.185-1.36170.2154-0.3370.43090.72850.2314-0.23541.3167-0.02-0.16890.889-0.04641.3669-3.8566-9.840933.4761
81.8741-0.64181.70770.8158-0.22131.78-0.5503-0.2369-0.12890.17040.1067-0.4992-0.21920.43040.3460.8939-0.06750.06981.22460.09591.081526.239525.5874-5.4205
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 77:162
2X-RAY DIFFRACTION2chain A and resid 1:76
3X-RAY DIFFRACTION3chain A and resid 163:388
4X-RAY DIFFRACTION4chain B and resid 77:162
5X-RAY DIFFRACTION5chain B and resid 1:76
6X-RAY DIFFRACTION6chain B and resid 163:388
7X-RAY DIFFRACTION7chain C
8X-RAY DIFFRACTION8chain D

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