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- PDB-3w3s: Crystal structure of A. aeolicus tRNASec in complex with M. kandl... -

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Basic information

Entry
Database: PDB / ID: 3w3s
TitleCrystal structure of A. aeolicus tRNASec in complex with M. kandleri SerRS
Components
  • Type-2 serine--tRNA ligase
  • selenocysteine tRNA
KeywordsLIGASE/RNA / class 2 aminoacyl-tRNA synthetase / transfer RNA / aminoacylation / selenocysteine incorporation / selenium metabolism / LIGASE-RNA complex
Function / homology
Function and homology information


: / selenocysteine biosynthetic process / serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
Alpha-Beta Plaits - #1920 / Serine-tRNA ligase type 2, archaea / Serine-tRNA ligase type 2, tRNA-binding domain / tRNA-binding domain / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. ...Alpha-Beta Plaits - #1920 / Serine-tRNA ligase type 2, archaea / Serine-tRNA ligase type 2, tRNA-binding domain / tRNA-binding domain / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE / : / RNA / RNA (> 10) / Type-2 serine--tRNA ligase
Similarity search - Component
Biological speciesMethanopyrus kandleri (archaea)
Aquifex aeolicus VF5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.095 Å
AuthorsItoh, Y. / Sekine, S. / Yokoyama, S.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Tertiary structure of bacterial selenocysteine tRNA
Authors: Itoh, Y. / Sekine, S. / Suetsugu, S. / Yokoyama, S.
History
DepositionDec 27, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Aug 7, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type-2 serine--tRNA ligase
B: selenocysteine tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,24727
Polymers94,0532
Non-polymers4,19325
Water0
1
A: Type-2 serine--tRNA ligase
B: selenocysteine tRNA
hetero molecules

A: Type-2 serine--tRNA ligase
B: selenocysteine tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,49454
Polymers188,1074
Non-polymers8,38750
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation43_455-x-1/2,-z+1/2,-y+1/21
Buried area18180 Å2
ΔGint-346 kcal/mol
Surface area75090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)272.817, 272.817, 272.817
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432

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Components

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Protein / RNA chain , 2 types, 2 molecules AB

#1: Protein Type-2 serine--tRNA ligase / Seryl-tRNA synthetase / SerRS / Seryl-tRNA(Ser/Sec) synthetase


Mass: 62155.410 Da / Num. of mol.: 1
Mutation: R55Y, E58Y, E62Y, R116Y, D118Y, E189R, D193R, E379Y, E383R, E497Y, E499Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanopyrus kandleri (archaea) / Strain: AV19 / Gene: serS / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / References: UniProt: Q8TVD2, serine-tRNA ligase
#2: RNA chain selenocysteine tRNA


Mass: 31897.924 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The tRNASec from Aquifex aeolicus VF5 was prepared by in vitro transcription with T7 RNA polymerase.
Source: (synth.) Aquifex aeolicus VF5 (bacteria) / References: GenBank: 6626248

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Non-polymers , 4 types, 25 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SSA / 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE


Mass: 433.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19N7O8S
#5: Chemical
ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Pt
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.5 Å3/Da / Density % sol: 72.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 100mM trisodium citrate-HCl, 1.3M ammonium sulfate, 210mM potassium sodium tartrate, 50mM imidazole, 400mM NaCl, 10mM MgCl2, 0.5mM 5'-O-[N-(L-seryl)sulfamoyl]adenosine, pH 5.6, VAPOR ...Details: 100mM trisodium citrate-HCl, 1.3M ammonium sulfate, 210mM potassium sodium tartrate, 50mM imidazole, 400mM NaCl, 10mM MgCl2, 0.5mM 5'-O-[N-(L-seryl)sulfamoyl]adenosine, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1901
2901
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-5A10.97848
SYNCHROTRONPhoton Factory AR-NE3A21.07186, 1.07227, 1.05404
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 315r1CCDNov 27, 2009mirrors
ADSC QUANTUM 2702CCDNov 4, 2009mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SiSINGLE WAVELENGTHMx-ray1
2SiMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.978481
21.071861
31.072271
41.054041
ReflectionResolution: 3.095→50 Å / Num. all: 31746 / Num. obs: 31714 / % possible obs: 99.9 % / Observed criterion σ(I): -2 / Redundancy: 15 % / Biso Wilson estimate: 102.66 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 28.4
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.847 / Mean I/σ(I) obs: 3.49 / Num. unique all: 3126 / Rsym value: 0.847 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 3.095→35.823 Å / Occupancy max: 1 / Occupancy min: 0.25 / SU ML: 0.83 / σ(F): 1.33 / Phase error: 25.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2603 1556 5.01 %random
Rwork0.2036 ---
obs0.2064 31040 97.83 %-
all-31729 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 90.343 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso max: 333.86 Å2 / Biso mean: 128.4284 Å2 / Biso min: 54.49 Å2
Refinement stepCycle: LAST / Resolution: 3.095→35.823 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4363 2090 85 0 6538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096871
X-RAY DIFFRACTIONf_angle_d1.2539799
X-RAY DIFFRACTIONf_chiral_restr0.0821133
X-RAY DIFFRACTIONf_plane_restr0.007894
X-RAY DIFFRACTIONf_dihedral_angle_d16.6342898
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0954-3.19520.32091350.306626932828100
3.1952-3.30940.34221440.27622671281599
3.3094-3.44180.37921520.2712596274897
3.4418-3.59830.31341260.24782590271695
3.5983-3.78780.25721330.21582617275096
3.7878-4.02480.24671580.20092568272696
4.0248-4.33510.23371420.17352635277797
4.3351-4.77040.22711180.16192720283899
4.7704-5.45860.22551720.17012715288799
5.4586-6.86940.24531390.19842746288599
6.8694-35.8250.27221370.21082933307099
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)
13.2925-0.8926-0.97318.71331.61854.0522-0.10980.0570.14750.50280.1596-0.15240.33520.2058-0.0690.52690.0882-0.03080.52680.00350.6431-37.6726-6.6932122.9804
23.46840.2985-0.19452.0961-0.21291.9735-0.29980.10070.91330.06890.1691-0.4845-0.24240.48110.09280.4137-0.0608-0.11540.652-0.02750.8353-57.46436.4384106.9978
35.4662-0.64510.17535.80592.91867.16750.47922.19620.2278-1.8439-0.05910.7965-0.6683-2.8343-0.21572.28190.0839-0.1833.53490.57892.1729-63.0994-22.530477.3505
49.039-0.6016-3.80282.84722.76673.8377-0.43952.09370.8095-1.0907-0.0232-0.59160.74310.3005-0.06951.5880.25010.01061.64220.12991.3921-40.5604-18.11885.2014
56.25720.20212.19131.0257-0.87131.55620.82552.2343-0.1233-0.0255-0.1076-0.35010.5502-0.0693-0.74581.35460.3197-0.10691.1525-0.14071.4186-30.4446-23.925390.5483
62.4727-2.1792.90611.9624-2.69794.52630.31052.40141.2413-1.2346-0.5314-0.8509-0.36151.48460.09071.50280.0644-0.07542.29990.26932.3285-5.6784-20.726381.0229
76.0787-4.45294.64673.2226-3.3943.54620.517-0.33510.6305-0.9330.4090.2249-1.4111-0.1759-0.58331.24070.0623-0.20351.64530.01981.7818-21.2746-20.33891.4766
83.52051.97211.19481.17490.26523.5283-0.29080.40730.2401-0.82760.08410.2419-0.27190.33490.21561.20890.02830.03330.7257-0.051.4098-32.5112-1.2982101.085
94.66871.7423-1.46493.116-2.2275.59870.06680.5762-0.3365-0.92520.29230.51940.4725-1.7978-0.37581.58040.0526-0.24441.379-0.06641.3626-53.4752-21.734598.7411
105.34921.67364.63138.26161.96684.03930.62132.7014-0.8757-0.23970.3280.95610.5604-0.547-0.99672.073-0.6825-0.08993.70180.27721.872-62.3271-20.818168.7175
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:163)A1 - 163
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 164:527)A164 - 527
3X-RAY DIFFRACTION3CHAIN B AND (RESSEQ 1:5A)B1 - 5
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 6:12)B6 - 12
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 13:31)B13 - 31
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 32:38)B32 - 38
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 39:44)B39 - 44
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 45:50)B45 - 50
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 51:67)B51 - 67
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 67A:75)B67 - 75

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