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

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Basic information

Entry
Database: PDB / ID: 4yco
TitleE. coli dihydrouridine synthase C (DusC) in complex with tRNAPhe
Components
  • tRNA-dihydrouridine synthase C
  • tRNAphe
KeywordsOXIDOREDUCTASE / tRNA modification
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 (E. coli)
Escherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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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: tRNA-dihydrouridine synthase C
C: tRNA-dihydrouridine synthase C
D: tRNAphe
E: tRNAphe
F: tRNAphe
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,93837
Polymers180,7976
Non-polymers2,14131
Water11,061614
1
A: tRNA-dihydrouridine synthase C
D: tRNAphe
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,97112
Polymers60,2662
Non-polymers70610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-82 kcal/mol
Surface area23370 Å2
MethodPISA
2
B: tRNA-dihydrouridine synthase C
E: tRNAphe
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,99613
Polymers60,2662
Non-polymers73011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-95 kcal/mol
Surface area21980 Å2
MethodPISA
3
C: tRNA-dihydrouridine synthase C
F: tRNAphe
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,97112
Polymers60,2662
Non-polymers70610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-87 kcal/mol
Surface area22830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.585, 176.895, 238.413
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-501-

HOH

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Components

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Protein / RNA chain , 2 types, 6 molecules ABCDEF

#1: Protein tRNA-dihydrouridine synthase C


Mass: 35779.992 Da / Num. of mol.: 3 / Mutation: C98A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: dusC, yohI, b2140, JW2128 / Plasmid: pET28a / Production host: Escherichia coli Bl21(DE3) (bacteria) / References: UniProt: P33371, Oxidoreductases
#2: RNA chain tRNAphe


Mass: 24485.539 Da / Num. of mol.: 3 / Mutation: C3G, G70C / Source method: obtained synthetically / Source: (synth.) Escherichia coli K-12 (bacteria) / References: GenBank: 731469900

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Non-polymers , 4 types, 645 molecules

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


Mass: 456.344 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / 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: 2.93 Å3/Da / Density % sol: 58.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 11% w/v PEG 6K, 100 mM HEPES, 200 mM MgCl2, 10 mM MnCl2,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→49.25 Å / Num. obs: 123558 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 37.209 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.033 / Net I/σ(I): 15.7 / Num. measured all: 556847 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.1-2.144.70.9991.72844660730.5230.522100
11.5-49.254.30.0259.835968420.9990.01198.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
Aimless0.1.27data scaling
PHASERphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BFA, 3L0U

4bfa

3l0u


Resolution: 2.1→49.21 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.2234 / WRfactor Rwork: 0.1924 / FOM work R set: 0.8521 / SU B: 8.962 / SU ML: 0.119 / SU R Cruickshank DPI: 0.1706 / SU Rfree: 0.1516 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2234 1241 1 %RANDOM
Rwork0.1924 ---
obs0.1927 122260 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 267.77 Å2 / Biso mean: 46.048 Å2 / Biso min: 22.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.41 Å20 Å20 Å2
2--3.34 Å20 Å2
3----0.93 Å2
Refinement stepCycle: final / Resolution: 2.1→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7257 4533 240 495 12525
Biso mean--46.64 44.58 -
Num. residues----1143
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.008128420.016
X-RAY DIFFRACTIONr_bond_other_d0.00195420.02
X-RAY DIFFRACTIONr_angle_refined_deg1.263185791.683
X-RAY DIFFRACTIONr_angle_other_deg0.993221003
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9329635
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.30435623.455
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.375130415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1257615
X-RAY DIFFRACTIONr_chiral_restr0.07720080.2
X-RAY DIFFRACTIONr_gen_planes_refined0.007115290.02
X-RAY DIFFRACTIONr_gen_planes_other0.00129050.02
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 88 -
Rwork0.311 8955 -
all-9043 -
obs--99.96 %
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)
12.62291.33710.60292.35020.07021.9782-0.056-0.1269-0.10540.18290.01940.09540.0341-0.11430.03660.27070.04550.0250.01940.01870.122221.971140.5762270.5453
21.510.19460.08831.33780.51381.54540.0139-0.1348-0.14880.21190.0516-0.22380.10070.1941-0.06550.29040.0384-0.02010.05750.05110.168233.764340.3191277.5671
33.89840.68690.55072.06290.68751.52110.04690.23690.1431-0.2241-0.1296-0.0649-0.10990.04530.08270.37630.0239-0.00930.03490.04140.20883.550887.6199284.8484
42.5619-0.53380.54541.419-0.21751.49030.06450.4647-0.1691-0.2498-0.09650.14410.1114-0.02370.0320.43020.0097-0.00520.0955-0.03210.2531-2.065377.5338277.4581
51.45480.853-0.15262.84940.11861.9608-0.04970.18990.10210.00130.02110.104-0.0913-0.0540.02860.21280.0191-0.00210.03420.02710.106925.053448.1212244.9988
69.238912.8677-2.456817.9231-3.42070.665-0.87890.4754-0.7112-1.24180.64-0.99960.2328-0.19480.23890.6778-0.0073-0.01910.7158-0.04050.561732.692857.2086229.8689
71.9327-0.15640.02812.28340.57472.1082-0.01460.33340.0736-0.19390.0632-0.2714-0.19780.3461-0.04870.245-0.03340.01770.14850.0370.165642.367849.4185240.5076
84.2279-0.62971.31811.076-0.45081.9310.0850.2327-0.4038-0.11410.0170.02270.2994-0.0673-0.1020.2986-0.01520.0250.0564-0.07240.183922.061130.1109233.7914
92.75451.32920.21281.14730.7660.9292-0.0711-0.2232-0.31770.1946-0.0303-0.02540.2307-0.00960.10140.39190.09250.04730.34130.07290.28879.889337.3708290.5439
1011.47821.60546.75420.23730.94243.9767-0.38040.5750.4604-0.06530.0967-0.0173-0.23180.3060.28370.5901-0.1254-0.10940.61350.10970.624-11.537649.4203270.3699
115.827-2.66092.5888.5425-1.20821.1716-0.7506-0.8088-0.35950.8571.02551.9479-0.3959-0.2911-0.27490.8532-0.04740.24760.7097-0.10791.05075.528248.9169290.6335
124.03711.4687-2.54271.6603-1.75532.5110.0526-0.2694-0.30350.0402-0.19720.07150.0910.01570.14460.3777-0.009-0.0160.31870.01790.205616.68539.8654302.915
1312.2315-6.28722.385911.7251-9.475413.2262-0.5793-0.7967-0.71730.03970.2786-0.64541.2481-0.81350.30070.85490.0133-0.06050.7916-0.05281.083411.334113.211309.8901
141.15861.10230.54911.53790.11480.7259-0.19720.4489-0.3846-0.68770.3278-0.49370.1640.2993-0.13060.8369-0.04190.10240.2425-0.0280.48610.632294.4302263.5161
150.25840.1830.05847.54132.79252.55330.0609-0.3856-0.02040.2917-0.2573-0.00620.1565-0.37450.19640.4434-0.07770.00860.6347-0.03040.31910.4117116.0065281.8817
161.91492.3579-0.182710.034.38833.5190.6941.32282.5401-1.0607-0.18672.42-1.0238-2.2194-0.50731.1360.6530.63032.71931.92753.52743.0371106.3557265.3717
174.55361.4198-2.62432.6325-1.62422.1953-0.05470.3964-0.2119-0.2237-0.0619-0.3250.29090.0050.11660.6473-0.0091-0.02890.31080.00430.33744.13393.9258252.5458
180.32120.0980.4213.16981.31731.04350.00240.26910.2006-0.2199-0.0916-0.2853-0.16750.24120.08930.4290.09220.01460.3630.14880.361520.834460.7432225.306
191.2987-3.1378-2.83477.76366.99316.3086-0.0671-0.0011-0.14660.3818-0.27140.28570.2774-0.26220.33861.172-0.15440.14630.613-0.14750.769-0.393373.0521246.6178
205.6574-2.9906-1.48331.61830.76710.40250.93941.915-0.7124-0.492-1.00380.5414-0.2123-0.55960.06440.73430.0241-0.07580.92510.01560.82398.719658.8559226.6376
210.6760.1611-0.62635.6323-1.94642.593-0.07660.04290.2302-0.0738-0.0562-0.4966-0.16260.21430.13280.34230.0298-0.0160.29670.03790.27422.938354.7524212.376
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 107
2X-RAY DIFFRACTION2A108 - 314
3X-RAY DIFFRACTION3B0 - 107
4X-RAY DIFFRACTION4B108 - 312
5X-RAY DIFFRACTION5C0 - 98
6X-RAY DIFFRACTION6C99 - 107
7X-RAY DIFFRACTION7C108 - 201
8X-RAY DIFFRACTION8C202 - 314
9X-RAY DIFFRACTION9D1 - 28
10X-RAY DIFFRACTION10D29 - 43
11X-RAY DIFFRACTION11D44 - 47
12X-RAY DIFFRACTION12D48 - 70
13X-RAY DIFFRACTION13D71 - 74
14X-RAY DIFFRACTION14E3 - 19
15X-RAY DIFFRACTION15E20 - 43
16X-RAY DIFFRACTION16E44 - 48
17X-RAY DIFFRACTION17E49 - 69
18X-RAY DIFFRACTION18F1 - 28
19X-RAY DIFFRACTION19F29 - 42
20X-RAY DIFFRACTION20F43 - 48
21X-RAY DIFFRACTION21F49 - 71

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