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- PDB-3b0u: tRNA-dihydrouridine synthase from Thermus thermophilus in complex... -

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Basic information

Entry
Database: PDB / ID: 3b0u
TitletRNA-dihydrouridine synthase from Thermus thermophilus in complex with tRNA fragment
Components
  • RNA (5'-R(*GP*GP*(H2U)P*A)-3')
  • tRNA-dihydrouridine synthase
KeywordsOXIDOREDUCTASE/RNA / Tim barrel / OXIDOREDUCTASE-RNA complex
Function / homology
Function and homology information


tRNA-dihydrouridine20a synthase activity / tRNA-dihydrouridine20 synthase [NAD(P)+] / tRNA-dihydrouridine20 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
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1460 / tRNA-dihydrouridine(20/20a) synthase / tRNA-dihydrouridine synthase / tRNA-dihydrouridine synthase, conserved site / DUS-like, FMN-binding domain / Dihydrouridine synthase (Dus) / Uncharacterized protein family UPF0034 signature. / Four Helix Bundle (Hemerythrin (Met), subunit A) / Aldolase class I / Aldolase-type TIM barrel ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1460 / tRNA-dihydrouridine(20/20a) synthase / tRNA-dihydrouridine synthase / tRNA-dihydrouridine synthase, conserved site / DUS-like, FMN-binding domain / Dihydrouridine synthase (Dus) / Uncharacterized protein family UPF0034 signature. / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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 / tRNA-dihydrouridine(20/20a) synthase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.948 Å
AuthorsYu, F. / Tanaka, Y. / Yamashita, K. / Nakamura, A. / Yao, M. / Tanaka, I.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Molecular basis of dihydrouridine formation on tRNA
Authors: Yu, F. / Tanaka, Y. / Yamashita, K. / Suzuki, T. / Nakamura, A. / Hirano, N. / Suzuki, T. / Yao, M. / Tanaka, I.
History
DepositionJun 14, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2011Group: Database references
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 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_conn / 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_conn.pdbx_leaving_atom_flag / _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: RNA (5'-R(*GP*GP*(H2U)P*A)-3')
B: RNA (5'-R(*GP*GP*(H2U)P*A)-3')
X: tRNA-dihydrouridine synthase
Y: tRNA-dihydrouridine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6946
Polymers81,7814
Non-polymers9132
Water7,530418
1
A: RNA (5'-R(*GP*GP*(H2U)P*A)-3')
X: tRNA-dihydrouridine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3473
Polymers40,8912
Non-polymers4561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-7 kcal/mol
Surface area13340 Å2
MethodPISA
2
B: RNA (5'-R(*GP*GP*(H2U)P*A)-3')
Y: tRNA-dihydrouridine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3473
Polymers40,8912
Non-polymers4561
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-7 kcal/mol
Surface area13400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.643, 126.643, 112.670
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11X-524-

HOH

21Y-528-

HOH

31Y-529-

HOH

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Components

#1: RNA chain RNA (5'-R(*GP*GP*(H2U)P*A)-3')


Mass: 1282.842 Da / Num. of mol.: 2 / Fragment: tRNA fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8
Description: the full length tRNA was transcripted in E. coli expression system and after binding to protein the RNA was processed by RNase
Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
#2: Protein tRNA-dihydrouridine synthase


Mass: 39607.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0016 / Plasmid: CDFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q5SMC7
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 2.13 Å3/Da / Density % sol: 42.15 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: HEPES, PEG 12000, pH 7.0, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 2, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.948→19.798 Å / Num. all: 49091 / Num. obs: 49091 / % possible obs: 99.7 % / Redundancy: 5.7 % / Rsym value: 0.065 / Net I/σ(I): 18.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.95-2.055.60.5820.5283.54000971320.2450.5820.5283.598.6
2.05-2.185.70.3710.3375.53869467680.1550.3710.3375.5100
2.18-2.335.70.2370.2158.43689364370.0990.2370.2158.4100
2.33-2.525.80.1610.14711.63408059200.0670.1610.14711.6100
2.52-2.765.80.1080.09815.93170254840.0450.1080.09815.9100
2.76-3.085.80.070.06421.42882049730.0290.070.06421.4100
3.08-3.565.80.0450.04131.62518343410.0190.0450.04131.6100
3.56-4.365.80.0330.0343.92154237100.0140.0330.0343.9100
4.36-6.165.80.0280.02550.71633928320.0120.0280.02550.7100
6.16-19.7985.60.0280.02554.1830614940.0120.0280.02554.195.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
MOLREPphasing
PHENIXdev_708refinement
PDB_EXTRACT3.1data extraction
SERGUIdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3B0P

3b0p


Resolution: 1.948→19.798 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8069 / SU ML: 0.54 / σ(F): 1.97 / Phase error: 25.83 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2198 2157 4.4 %RANDOM
Rwork0.1806 ---
obs0.1823 49073 99.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.608 Å2 / ksol: 0.385 e/Å3
Displacement parametersBiso max: 126.02 Å2 / Biso mean: 31.6774 Å2 / Biso min: 10.75 Å2
Baniso -1Baniso -2Baniso -3
1--2.8948 Å20 Å20 Å2
2---2.8948 Å20 Å2
3---5.7895 Å2
Refinement stepCycle: LAST / Resolution: 1.948→19.798 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4968 170 62 418 5618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065344
X-RAY DIFFRACTIONf_angle_d0.6837258
X-RAY DIFFRACTIONf_chiral_restr0.05798
X-RAY DIFFRACTIONf_plane_restr0.003920
X-RAY DIFFRACTIONf_dihedral_angle_d12.9652090
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9484-1.99370.27471360.22333054319097
1.9937-2.04350.2921440.220731493293100
2.0435-2.09870.24861380.220531443282100
2.0987-2.16040.24371530.194430963249100
2.1604-2.230.23111440.193931763320100
2.23-2.30960.2031420.1831093251100
2.3096-2.4020.27541490.185831263275100
2.402-2.51110.21611380.184231183256100
2.5111-2.64320.25771540.178631463300100
2.6432-2.80830.23051380.184231363274100
2.8083-3.02450.22381450.181531493294100
3.0245-3.32750.19791480.187631303278100
3.3275-3.80610.21651420.174231343276100
3.8061-4.78410.19991450.155231353280100
4.7841-19.7990.18791410.17333114325599
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)
11.23220.6960.22230.90040.1962.01190.1491-0.1094-0.22250.0924-0.01460.07810.2026-0.1882-0.12150.1661-0.023-0.03690.20090.00570.1703-28.1969-19.54626.2713
20.9337-0.0955-0.10941.8940.13771.84020.0628-0.2977-0.03620.4243-0.00150.41420.229-0.4224-0.06590.2428-0.05210.03460.2780.05690.1567-27.334-16.678640.4193
31.55340.1222-0.17121.05280.07380.88310.0214-0.17910.06020.223-0.0094-0.098-0.0115-0.0631-0.02390.182-0.0111-0.00710.1566-0.00340.0955-15.4019-6.145634.5724
41.89310.3270.61911.43320.22412.26760.12890.2616-0.0187-0.240.031-0.13470.0088-0.0006-0.13850.1647-0.01450.01030.1585-0.00890.0946-14.0148-11.118820.6951
51.7162-0.58620.1111.04450.00131.02420.14650.3451-0.2075-0.1537-0.0948-0.05860.07580.1112-0.05890.15750.026-0.01350.2389-0.03970.1097-23.1819-18.425715.4361
61.79760.39410.09621.36230.04372.3620.16050.1102-0.2993-0.132-0.07360.32850.1686-0.4238-0.07520.1433-0.0385-0.07440.3275-0.01180.2579-43.818-21.773116.117
71.264-0.2265-0.08830.9540.20131.5954-0.03060.04640.02850.06760.0587-0.2530.06950.0867-0.04210.15870.0242-0.00810.2-0.02840.2877-32.376521.929611.8925
82.3757-0.0847-0.21871.87360.08251.67770.0675-0.342-0.07360.41860.0082-0.2550.15370.2-0.04790.21910.0198-0.07570.190.01490.2151-35.2921.131825.998
91.5685-0.34840.08791.6121-0.36550.8785-0.0086-0.26150.08610.23250.05170.16180.0095-0.066-0.05160.16160.0010.02650.1873-0.01230.2048-48.895726.806323.3772
101.9567-0.3872-0.5881.42780.41410.93070.05520.29590.1189-0.242-0.0413-0.0729-0.0451-0.0971-0.00930.15320.01080.00340.19340.02170.1853-44.03526.85955.3888
111.0739-0.7181-0.14591.4297-0.1761.89230.0760.24560.01-0.1948-0.0018-0.57590.27420.35140.02450.21060.0780.03910.2567-0.13140.4754-22.72849.50051.6668
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'X' and (resseq 2:38)X2 - 38
2X-RAY DIFFRACTION2chain 'X' and (resseq 39:110)X39 - 110
3X-RAY DIFFRACTION3chain 'X' and (resseq 111:194)X111 - 194
4X-RAY DIFFRACTION4chain 'X' and (resseq 195:217)X195 - 217
5X-RAY DIFFRACTION5chain 'X' and (resseq 218:250)X218 - 250
6X-RAY DIFFRACTION6chain 'X' and (resseq 251:313)X251 - 313
7X-RAY DIFFRACTION7chain 'Y' and (resseq 2:38)Y2 - 38
8X-RAY DIFFRACTION8chain 'Y' and (resseq 39:110)Y39 - 110
9X-RAY DIFFRACTION9chain 'Y' and (resseq 111:175)Y111 - 175
10X-RAY DIFFRACTION10chain 'Y' and (resseq 176:250)Y176 - 250
11X-RAY DIFFRACTION11chain 'Y' and (resseq 251:313)Y251 - 313

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