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

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Basic information

Entry
Database: PDB / ID: 3wqz
TitleCrystal structure of Archaeoglobus fulgidus alanyl-tRNA synthetase in complex with a tRNA(Ala) variant having A3.U70
Components
  • Alanine--tRNA ligase
  • RNA (75-MER)
KeywordsLIGASE/RNA / aminoacyl-tRNA synthetases / protein-RNA complex / homodimer / 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: 3.489 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 / pdbx_struct_conn_angle / struct_conn / struct_site
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_label_asym_id / _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)230,5717
Polymers229,6063
Non-polymers9664
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10740 Å2
ΔGint-128 kcal/mol
Surface area93220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.609, 169.676, 176.649
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: 24246.479 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 3.25 Å3/Da / Density % sol: 62.16 %
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: Oct 14, 2012 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.489→50 Å / Num. all: 38881 / Num. obs: 38839 / % possible obs: 99 % / Observed criterion σ(I): -1 / Redundancy: 6.8 % / Biso Wilson estimate: 99.19 Å2 / Rsym value: 0.12
Reflection shellResolution: 3.489→3.63 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 2.54 / Num. unique all: 4015 / Rsym value: 0.689 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.489→42.738 Å / SU ML: 0.49 / σ(F): 1.38 / Phase error: 29.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2765 1995 5.15 %RANDOM
Rwork0.2413 ---
obs0.2431 38766 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 120.58 Å2
Refinement stepCycle: LAST / Resolution: 3.489→42.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14412 1608 58 0 16078
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416545
X-RAY DIFFRACTIONf_angle_d0.76222706
X-RAY DIFFRACTIONf_dihedral_angle_d13.5786509
X-RAY DIFFRACTIONf_chiral_restr0.0262539
X-RAY DIFFRACTIONf_plane_restr0.0142668
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4895-3.57670.36011380.35252594273299
3.5767-3.67340.37871540.32525812735100
3.6734-3.78140.3181280.304825892717100
3.7814-3.90340.33771340.297825952729100
3.9034-4.04280.31641500.288625872737100
4.0428-4.20450.32921420.26525952737100
4.2045-4.39570.3281450.265126112756100
4.3957-4.62720.30881460.242725912737100
4.6272-4.91670.24131180.22226502768100
4.9167-5.29560.26781430.22226332776100
5.2956-5.82740.28641480.250926332781100
5.8274-6.66790.27531610.252426422803100
6.6679-8.39040.24571400.215926892829100
8.3904-42.74160.19711480.17892781292999
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)
12.2898-0.5491-0.31072.71680.24233.08580.0625-0.3670.68040.17940.21580.3062-0.1415-0.1489-0.1270.79330.25780.11260.7792-0.2911.0053-64.961531.591935.5379
21.82-1.86190.27563.3762-0.09092.92630.27380.51640.3672-0.758-0.24550.0326-0.1494-0.3426-0.01150.64490.16280.17660.80240.02740.6841-58.766118.72549.293
3-0.48-1.13090.70680.4073-0.28950.3540.0383-0.0602-0.18050.04340.45160.96780.10720.0037-0.19681.75150.06310.14482.1286-0.00511.4806-50.4665-8.092956.0835
42.8811-2.13551.23852.1654-1.59764.005-0.2575-0.22350.16740.2768-0.1496-0.24220.2743-0.03760.29970.56010.0370.01440.8009-0.09320.7961-35.01413.43537.9268
51.77160.21021.05781.1030.47210.98690.0740.2233-0.260.24680.12820.05620.23050.1018-0.09860.476-0.04030.09390.6337-0.05950.3137-47.0209-28.267911.2291
61.2395-1.0708-1.07670.93090.37881.3833-0.55910.1121.2747-0.32270.03060.52150.390.52670.2691.69210.2511-0.9531.8847-0.38522.704336.2923-37.713169.1793
73.4622-1.09311.65.8448-0.35432.0258-0.5708-0.25690.24250.80150.4699-1.0980.42240.24580.09980.77580.2302-0.23570.6368-0.10960.698713.8345-40.027459.6903
81.3304-0.3578-0.00330.9849-0.26160.7622-0.26770.45150.3021-0.90250.051-0.7088-0.08440.12720.14671.1759-0.2529-0.21280.86580.00961.23398.626-18.952334.2448
92.87990.31571.20253.60770.62.2315-0.3728-0.17330.7097-0.3928-0.02110.066-0.5291-0.13750.16980.7888-0.0213-0.44120.5083-0.0351.0238-6.9189-14.110645.1178
102.0966-1.63091.3520.15490.95223.1834-0.2503-0.01330.18880.1831-0.2902-0.2543-0.0795-0.34280.21340.5448-0.095-0.08220.5566-0.00780.48-24.9059-24.580619.6563
113.0453-1.0303-0.39351.7096-0.00052.794-0.20210.46970.4405-0.1387-0.0777-0.29980.4924-0.64710.14711.04060.2169-0.2261.0982-0.30640.7886-27.1216-56.3655-20.7356
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:265)A2 - 265
2X-RAY DIFFRACTION2chain 'A' and (resseq 266:478)A266 - 478
3X-RAY DIFFRACTION3chain 'A' and (resseq 479:589)A479 - 589
4X-RAY DIFFRACTION4chain 'A' and (resseq 590:676)A590 - 676
5X-RAY DIFFRACTION5chain 'A' and (resseq 677:906)A677 - 906
6X-RAY DIFFRACTION6chain 'B' and (resseq 1:42)B1 - 42
7X-RAY DIFFRACTION7chain 'B' and (resseq 43:404)B43 - 404
8X-RAY DIFFRACTION8chain 'B' and (resseq 405:589)B405 - 589
9X-RAY DIFFRACTION9chain 'B' and (resseq 590:702)B590 - 702
10X-RAY DIFFRACTION10chain 'B' and (resseq 703:800)B703 - 800
11X-RAY DIFFRACTION11chain 'B' and (resseq 801:904)B801 - 904

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