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- PDB-3wqy: Crystal structure of Archaeoglobus fulgidus alanyl-tRNA synthetas... -

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Basic information

Entry
Database: PDB / ID: 3wqy
TitleCrystal structure of Archaeoglobus fulgidus alanyl-tRNA synthetase in complex with wild-type tRNA(Ala) having G3.U70
Components
  • Alanine--tRNA ligase
  • RNA (75-MER)
KeywordsLIGASE/RNA / aminoacyl-tRNA synthetases / protein-RNA complex / ligase / alanyladenylate analogue / LIGASE-RNA complex
Function / homology
Function and homology information


alanine-tRNA ligase / alanine-tRNA ligase activity / alanyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / tRNA binding / negative regulation of DNA-templated transcription / zinc ion binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
Diaminopimelate Epimerase; Chain A, domain 1 - #40 / Alanine-tRNA ligase, archaea / Elongation Factor Tu (Ef-tu); domain 3 - #130 / Replication Terminator Protein; Chain A, domain 2 - #20 / Threonyl-trna Synthetase; Chain A, domain 2 / Replication Terminator Protein; Chain A, domain 2 / Alanine-tRNA ligase, class IIc / Alanine-tRNA ligase, class IIc, anti-codon-binding domain superfamily / Alanyl-tRNA synthetase, class IIc, N-terminal / Alanyl-tRNA synthetase, class IIc, core domain ...Diaminopimelate Epimerase; Chain A, domain 1 - #40 / Alanine-tRNA ligase, archaea / Elongation Factor Tu (Ef-tu); domain 3 - #130 / Replication Terminator Protein; Chain A, domain 2 - #20 / Threonyl-trna Synthetase; Chain A, domain 2 / Replication Terminator Protein; Chain A, domain 2 / Alanine-tRNA ligase, class IIc / Alanine-tRNA ligase, class IIc, anti-codon-binding domain superfamily / Alanyl-tRNA synthetase, class IIc, N-terminal / Alanyl-tRNA synthetase, class IIc, core domain / tRNA synthetases class II (A) / Alanyl-transfer RNA synthetases family profile. / Threonyl-tRNA Synthetase; Chain A, domain 2 / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl and Alanyl tRNA synthetase second additional domain / DHHA1 domain / DHHA1 domain / Diaminopimelate Epimerase; Chain A, domain 1 / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Elongation Factor Tu (Ef-tu); domain 3 / Translation protein, beta-barrel domain superfamily / Roll / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
'5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE / RNA / RNA (> 10) / Alanine--tRNA ligase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsNaganuma, M. / Sekine, S. / Yokoyama, S.
CitationJournal: Nature / Year: 2014
Title: The selective tRNA aminoacylation mechanism based on a single G.U pair
Authors: Naganuma, M. / Sekine, S. / Chong, Y.E. / Guo, M. / Yang, X.L. / Gamper, H. / Hou, Y.M. / Schimmel, P. / Yokoyama, S.
History
DepositionFeb 5, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Alanine--tRNA ligase
B: Alanine--tRNA ligase
C: RNA (75-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,5298
Polymers229,6223
Non-polymers9085
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10830 Å2
ΔGint-92 kcal/mol
Surface area91940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.742, 169.836, 175.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Alanine--tRNA ligase / Alanyl-tRNA synthetase / AlaRS


Mass: 102679.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: AF_2255, alaS / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta2 / References: UniProt: O28029, alanine-tRNA ligase
#2: RNA chain RNA (75-MER)


Mass: 24262.479 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Archaeoglobus fulgidus (archaea)
#3: Chemical ChemComp-A5A / '5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE


Mass: 417.398 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H19N7O7S
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.23 Å3/Da / Density % sol: 61.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG 6000, citrate buffer, CdCl2, MPD, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 14, 2012
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. all: 45965 / Num. obs: 45365 / % possible obs: 99.6 % / Observed criterion σ(I): -1 / Redundancy: 5.4 % / Rsym value: 0.141
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 2.25 / Num. unique all: 4570 / Rsym value: 0.654 / % possible all: 99.3

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→41.765 Å / SU ML: 0.51 / σ(F): 1.38 / Phase error: 30.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2893 2329 5.14 %RANDOM
Rwork0.2503 ---
obs0.2523 45304 99.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 96.88 Å2
Refinement stepCycle: LAST / Resolution: 3.3→41.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14421 1609 59 7 16096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00616555
X-RAY DIFFRACTIONf_angle_d0.88622720
X-RAY DIFFRACTIONf_dihedral_angle_d15.8796521
X-RAY DIFFRACTIONf_chiral_restr0.0352538
X-RAY DIFFRACTIONf_plane_restr0.0152670
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2989-3.36620.38991210.37752432255397
3.3662-3.43940.36281310.354725112642100
3.4394-3.51940.35931470.354424552602100
3.5194-3.60730.33311380.33252488262699
3.6073-3.70480.38221440.32032507265199
3.7048-3.81370.32871180.298125102628100
3.8137-3.93680.3311400.284525162656100
3.9368-4.07730.29331340.270324802614100
4.0773-4.24040.33231460.246624942640100
4.2404-4.43320.29771400.240625162656100
4.4332-4.66670.24051320.224325232655100
4.6667-4.95860.24641150.206525692684100
4.9586-5.34080.26761430.21925462689100
5.3408-5.87690.26371490.236425512700100
5.8769-6.72430.26681500.249525632713100
6.7243-8.46030.27261370.216726052742100
8.4603-41.76780.22981440.18212709285399
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)
10.0176-0.03020.00040.02420.00190.003-0.0334-0.06480.0643-0.0096-0.1501-0.0529-0.0387-0.002400.62110.23070.07830.5219-0.21120.5586-76.237539.439332.4297
2-0.0274-0.0897-0.05370.026-0.1212-0.0083-0.09260.40710.6487-0.23730.0589-0.0240.0342-0.0991-0-0.73971.23570.87-1.146-1.052-0.4398-59.982824.549123.2599
30.0088-0.1579-0.057-0.1199-0.00950.0080.17020.0438-0.09020.2446-0.1750.17110.0001-0.1686-0-0.14660.28790.08620.1181-0.31740.1077-47.6994-4.621745.9912
40.11-0.10720.12380.00270.02470.0195-0.08290.11840.01460.1262-0.04790.03870.1080.13100.09910.04010.0109-0.1048-0.5062-0.3434-44.9641-22.798815.5284
5-0.00020.02750.0210.04170.0090.0235-0.122-0.019-0.02240.0063-0.0135-0.05390.09840.0055-00.19510.1833-0.0655-0.0081-0.15130.228221.5984-35.129266.41
60.082-0.08830.06070.0561-0.04790.0911-0.5278-0.02280.034-0.19030.3014-0.28520.5936-0.2858-00.20280.3325-0.0979-0.1154-0.05430.266513.0406-41.548856.7437
70.11330.01830.0066-0.00020.03030.0657-0.13420.12830.0846-0.0638-0.13350.04980.05320.257900.6418-0.0656-0.03670.31310.0420.559511.1754-15.716832.896
80.0137-0.04830.01160.03480.01240.0008-0.00540.02140.03340.0265-0.0177-0.0276-0.1055-0.135300.28-0.1269-0.4039-0.5731-0.38180.3995-6.5422-13.942744.5787
9-0.0981-0.04310.09190.0543-0.10640.07750.14340.39790.3142-0.1004-0.4553-0.06260.00820.0517-0-0.1371-0.4411-0.4971-0.5803-0.9612-0.6253-26.2576-40.8934-0.6675
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:61)A2 - 61
2X-RAY DIFFRACTION2chain 'A' and (resseq 62:466)A62 - 466
3X-RAY DIFFRACTION3chain 'A' and (resseq 467:641)A467 - 641
4X-RAY DIFFRACTION4chain 'A' and (resseq 642:906)A642 - 906
5X-RAY DIFFRACTION5chain 'B' and (resseq 1:108)B1 - 108
6X-RAY DIFFRACTION6chain 'B' and (resseq 109:424)B109 - 424
7X-RAY DIFFRACTION7chain 'B' and (resseq 425:589)B425 - 589
8X-RAY DIFFRACTION8chain 'B' and (resseq 590:701)B590 - 701
9X-RAY DIFFRACTION9chain 'B' and (resseq 702:905)B702 - 905

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