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- PDB-1eiy: THE CRYSTAL STRUCTURE OF PHENYLALANYL-TRNA SYNTHETASE FROM THERMU... -

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Basic information

Entry
Database: PDB / ID: 1eiy
TitleTHE CRYSTAL STRUCTURE OF PHENYLALANYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH COGNATE TRNAPHE
Components
  • (PHENYLALANYL-TRNA SYNTHETASE) x 2
  • TRNA(PHE)
KeywordsLIGASE/RNA / aminoacyl-tRNA synthetase / tRNA recognition / LIGASE-RNA COMPLEX
Function / homology
Function and homology information


phenylalanine-tRNA ligase / phenylalanine-tRNA ligase activity / phenylalanyl-tRNA aminoacylation / tRNA binding / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Phenylalanyl-tRNA Synthetase; Chain B, domain 1 - #10 / Phenylalanyl-tRNA Synthetase; Chain B, domain 3 / Phenylalanyl-trna Synthetase, Chain B, domain 3 / Ferrodoxin-fold anticodon-binding domain / Phenylalanine-tRNA ligase, class II, N-terminal / Phenylalanine-tRNA ligase alpha chain 1, bacterial / Aminoacyl tRNA synthetase class II, N-terminal domain / Phenylalanine-tRNA ligase, class IIc, beta subunit, bacterial type / Phenylalanyl-tRNA synthetase, class IIc, alpha subunit / Phenylalanly tRNA synthetase, tRNA-binding-domain ...Phenylalanyl-tRNA Synthetase; Chain B, domain 1 - #10 / Phenylalanyl-tRNA Synthetase; Chain B, domain 3 / Phenylalanyl-trna Synthetase, Chain B, domain 3 / Ferrodoxin-fold anticodon-binding domain / Phenylalanine-tRNA ligase, class II, N-terminal / Phenylalanine-tRNA ligase alpha chain 1, bacterial / Aminoacyl tRNA synthetase class II, N-terminal domain / Phenylalanine-tRNA ligase, class IIc, beta subunit, bacterial type / Phenylalanyl-tRNA synthetase, class IIc, alpha subunit / Phenylalanly tRNA synthetase, tRNA-binding-domain / tRNA synthetase, B5-domain / Phenylalanine-tRNA ligase, class IIc, beta subunit / tRNA synthetase B5 domain / B5 domain profile. / tRNA synthetase B5 domain / B3/4 domain / Ferrodoxin-fold anticodon-binding domain / Ferrodoxin-fold anticodon-binding domain superfamily / Ferredoxin-fold anticodon binding domain / Ferredoxin-fold anticodon binding (FDX-ACB) domain profile. / Ferredoxin-fold anticodon binding domain / B3/B4 tRNA-binding domain / Phenylalanyl-tRNA synthetase-like, B3/B4 / Phenylalanyl tRNA synthetase beta chain, core domain / Phenylalanyl tRNA synthetase beta chain CLM domain / B3/4 domain / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Phenylalanyl-tRNA synthetase / tRNA synthetases class II core domain (F) / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Putative DNA-binding domain superfamily / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Nucleic acid-binding proteins / 3-Layer(bba) Sandwich / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Plaits / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Phenylalanine--tRNA ligase alpha subunit / Phenylalanine--tRNA ligase beta subunit / Phenylalanine--tRNA ligase alpha subunit
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.3 Å
AuthorsGoldgur, Y. / Mosyak, L. / Reshetnikova, L. / Ankilova, V. / Safro, M.
CitationJournal: Structure / Year: 1997
Title: The crystal structure of phenylalanyl-tRNA synthetase from thermus thermophilus complexed with cognate tRNAPhe.
Authors: Goldgur, Y. / Mosyak, L. / Reshetnikova, L. / Ankilova, V. / Lavrik, O. / Khodyreva, S. / Safro, M.
History
DepositionFeb 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: TRNA(PHE)
A: PHENYLALANYL-TRNA SYNTHETASE
B: PHENYLALANYL-TRNA SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)150,5143
Polymers150,5143
Non-polymers00
Water0
1
C: TRNA(PHE)
A: PHENYLALANYL-TRNA SYNTHETASE
B: PHENYLALANYL-TRNA SYNTHETASE

C: TRNA(PHE)
A: PHENYLALANYL-TRNA SYNTHETASE
B: PHENYLALANYL-TRNA SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)301,0296
Polymers301,0296
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)175.0, 175.0, 140.6
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number154
Cell settingtrigonal
Space group name H-MP3221

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Components

#1: RNA chain TRNA(PHE)


Mass: 24484.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SGX1
#2: Protein PHENYLALANYL-TRNA SYNTHETASE / E.C.6.1.1.20 / PHENYLALANINE--TRNA LIGASE ALPHA CHAIN / PHERS


Mass: 39309.199 Da / Num. of mol.: 1 / Fragment: ALPHA CHAIN / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
References: UniProt: P27001, UniProt: Q5SGX2*PLUS, phenylalanine-tRNA ligase
#3: Protein PHENYLALANYL-TRNA SYNTHETASE / E.C.6.1.1.20 / PHENYLALANINE--TRNA LIGASE BETA CHAIN / PHERS


Mass: 86720.656 Da / Num. of mol.: 1 / Fragment: BETA CHAIN / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
References: UniProt: Q5SGX2, UniProt: Q5SGX1*PLUS, phenylalanine-tRNA ligase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 4.13 Å3/Da / Density % sol: 70.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: ammonium sulphate, magnesium sulphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP at 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MgSO411
2(NH4)2SO411
3MgSO412
4(NH4)2SO412
Crystal grow
*PLUS
Details: Reshetnikova, L., (1993) J. Mol. Biol., 231, 927.
Components of the solutions
*PLUS
IDCrystal-ID
11
21
31
41

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceSiteBeamlineTypeIDWavelength
ROTATING ANODERIGAKU RU20011.5418
SYNCHROTRONLURE D41A20.99
Detector
TypeIDDetectorDate
XENTRONICS1AREA DETECTOROct 10, 1992
MARRESEARCH2IMAGE PLATEOct 10, 1993
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.991
ReflectionResolution: 3.3→28 Å / Num. obs: 33340 / % possible obs: 86.3 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.158
Reflection shellResolution: 3.3→3.4 Å / Rmerge(I) obs: 0.338 / % possible all: 48
Reflection
*PLUS
Highest resolution: 3.28 Å / Lowest resolution: 28 Å
Reflection shell
*PLUS
% possible obs: 48 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
DENZOdata reduction
X-GENdata scaling
X-PLORphasing
RefinementResolution: 3.3→28 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1667 5 %random
Rwork0.221 ---
obs-33340 86.3 %-
Refinement stepCycle: LAST / Resolution: 3.3→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8862 1623 0 0 10485
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.025
X-RAY DIFFRACTIONx_angle_deg2.3
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 28 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 2.3

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