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- PDB-4ycp: E. coli dihydrouridine synthase C (DusC) in complex with tRNATrp -

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Basic information

Entry
Database: PDB / ID: 4ycp
TitleE. coli dihydrouridine synthase C (DusC) in complex with tRNATrp
Components
  • tRNA-dihydrouridine synthase C
  • tRNATrp
KeywordsOxidoreductase/RNA / tRNA modification / oxidoreductase-RNA complex
Function / homology
Function and homology information


tRNA-dihydrouridine16 synthase activity / tRNA dihydrouridine synthesis / tRNA dihydrouridine synthase activity / Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / FMN binding / flavin adenine dinucleotide binding / tRNA binding
Similarity search - Function
Dihydrouridine synthase, C-terminal recognition domain / tRNA-dihydrouridine(16) synthase / tRNA-dihydrouridine(16) synthase, C-terminal / tRNA-dihydrouridine synthase / Bacteriocin As-48; Chain A / tRNA-dihydrouridine synthase, conserved site / DUS-like, FMN-binding domain / Dihydrouridine synthase (Dus) / Uncharacterized protein family UPF0034 signature. / Aldolase class I ...Dihydrouridine synthase, C-terminal recognition domain / tRNA-dihydrouridine(16) synthase / tRNA-dihydrouridine(16) synthase, C-terminal / tRNA-dihydrouridine synthase / Bacteriocin As-48; Chain A / tRNA-dihydrouridine synthase, conserved site / DUS-like, FMN-binding domain / Dihydrouridine synthase (Dus) / Uncharacterized protein family UPF0034 signature. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / : / RNA / RNA (> 10) / tRNA-dihydrouridine(16) synthase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsByrne, R.T. / Jenkins, H.T. / Peters, D.T. / Whelan, F. / Stowell, J. / Aziz, N. / Kasatsky, P. / Rodnina, M.V. / Koonin, E.V. / Konevega, A.L. / Antson, A.A.
Funding support United Kingdom, Russian Federation, 3items
OrganizationGrant numberCountry
Wellcome Trust098230 United Kingdom
RFBR13-04-40212-H comfi Russian Federation
RSF14-34-00023 Russian Federation
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Major reorientation of tRNA substrates defines specificity of dihydrouridine synthases.
Authors: Byrne, R.T. / Jenkins, H.T. / Peters, D.T. / Whelan, F. / Stowell, J. / Aziz, N. / Kasatsky, P. / Rodnina, M.V. / Koonin, E.V. / Konevega, A.L. / Antson, A.A.
History
DepositionFeb 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2May 20, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA-dihydrouridine synthase C
B: tRNATrp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9156
Polymers60,2422
Non-polymers6734
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-57 kcal/mol
Surface area20960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.516, 98.516, 231.172
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-508-

HOH

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Components

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Protein / RNA chain , 2 types, 2 molecules AB

#1: Protein tRNA-dihydrouridine synthase C / DusC


Mass: 35779.992 Da / Num. of mol.: 1 / Fragment: UNP residues 1-315 / Mutation: C98A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: dusC, yohI, b2140, JW2128 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P33371, Oxidoreductases
#2: RNA chain tRNATrp


Mass: 24462.500 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli K-12 (bacteria) / References: GenBank: 731469900

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Non-polymers , 4 types, 56 molecules

#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.69 Å3/Da / Density % sol: 54.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-Tris pH 6.5, 0.2 M Li2SO4 26% PEG 2K MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 5, 2014
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 2.55→49.26 Å / Num. obs: 22329 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 44.936 Å2 / Rmerge(I) obs: 0.141 / Net I/σ(I): 8.8
Reflection shellResolution: 2.55→2.66 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.099 / Mean I/σ(I) obs: 1.5 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4bfa

4bfa


Resolution: 2.55→49.26 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.914 / SU B: 21.303 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.427 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1127 5 %RANDOM
Rwork0.2081 ---
obs0.2095 21202 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.39 Å2 / Biso mean: 49.616 Å2 / Biso min: 24.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å2-0.26 Å20 Å2
2---0.52 Å20 Å2
3---1.7 Å2
Refinement stepCycle: final / Resolution: 2.55→49.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2398 1287 42 52 3779
Biso mean--46.32 38.73 -
Num. residues----370
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.00639260.016
X-RAY DIFFRACTIONr_bond_other_d0.00229740.02
X-RAY DIFFRACTIONr_angle_refined_deg1.00356211.689
X-RAY DIFFRACTIONr_angle_other_deg1.04468843
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5783214.86
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22211223.839
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.99440915
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9982115
X-RAY DIFFRACTIONr_chiral_restr0.0616200.2
X-RAY DIFFRACTIONr_gen_planes_refined0.00436240.02
X-RAY DIFFRACTIONr_gen_planes_other0.0018840.02
X-RAY DIFFRACTIONr_mcbond_it0.31812302.673
X-RAY DIFFRACTIONr_mcbond_other0.31812292.673
X-RAY DIFFRACTIONr_mcangle_it0.56215344.008
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 93 -
Rwork0.321 1534 -
all-1627 -
obs--99.69 %
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)
12.1395-0.39080.40312.84110.47742.963-0.0587-0.23610.03-0.04430.0155-0.11150.2076-0.20140.04320.072-0.0670.00370.198-0.00880.006327.7179-42.2182-4.3455
21.9897-0.15890.19252.11010.65643.2542-0.0419-0.2047-0.22090.15120.0872-0.11570.62970.2348-0.04530.1714-0.02390.00750.2080.0130.040436.3254-50.713-7.3043
33.4707-1.406-0.90492.06120.52172.6492-0.0985-0.18960.2570.08540.1658-0.3367-0.30280.2638-0.06730.1054-0.084-0.06280.2355-0.03460.12739.2024-32.1907-0.5191
43.8271.1705-1.27716.0735-1.16122.5255-0.0031-0.17650.42850.50970.1320.2966-0.6593-0.619-0.1290.25050.13660.01270.413-0.05040.057817.7742-30.413310.2686
50.17260.7768-0.05236.47010.95570.5126-0.0349-0.111-0.12370.2132-0.112-0.29440.21810.12140.1470.303-0.1055-0.00340.35620.07920.182625.105-55.83312.3847
65.3225-0.4140.09063.42641.06581.05070.07790.6801-0.1106-0.3552-0.34020.8822-0.1247-0.45280.26230.4459-0.074-0.11590.4717-0.04410.31249.6601-66.0161-1.413
73.1931-2.7799-0.73613.72682.17961.9877-0.08390.23890.4833-0.2745-0.1342-0.1829-0.41610.00160.21820.6845-0.0112-0.10510.5973-0.16850.62836.7879-70.9474-8.5474
817.52463.303316.57530.63613.103815.7174-0.5703-1.08670.8746-0.0231-0.22770.1784-0.6897-1.04780.7980.63150.0529-0.03750.4893-0.12870.513811.8122-58.81885.8729
90.3160.9911-0.36375.4445-3.61593.48620.0593-0.0733-0.15520.5085-0.1136-0.33310.0297-0.04450.05420.4918-0.04480.01850.3552-0.0180.132525.4969-52.594325.1533
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 45
2X-RAY DIFFRACTION2A46 - 163
3X-RAY DIFFRACTION3A164 - 257
4X-RAY DIFFRACTION4A258 - 315
5X-RAY DIFFRACTION5B5 - 21
6X-RAY DIFFRACTION6B22 - 32
7X-RAY DIFFRACTION7B36 - 42
8X-RAY DIFFRACTION8B43 - 47
9X-RAY DIFFRACTION9B48 - 69

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