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- PDB-1jjc: Crystal structure at 2.6A resolution of phenylalanyl-tRNA synthet... -

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Basic information

Entry
Database: PDB / ID: 1jjc
TitleCrystal structure at 2.6A resolution of phenylalanyl-tRNA synthetase complexed with phenylalanyl-adenylate in the presence of manganese
Components(PHENYLALANYL-TRNA SYNTHETASE ...) x 2
KeywordsLIGASE / Heterodimer / phenylalanyl-tRNA / Thermus thermophilus
Function / homology
Function and homology information


phenylalanine-tRNA ligase complex / phenylalanine-tRNA ligase / phenylalanyl-tRNA aminoacylation / phenylalanine-tRNA ligase activity / tRNA binding / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Phenylalanyl-tRNA Synthetase; Chain B, domain 3 / Phenylalanyl-trna Synthetase, Chain B, domain 3 / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 - #10 / 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 3 / Phenylalanyl-trna Synthetase, Chain B, domain 3 / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 - #10 / 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 / tRNA synthetase B5 domain / B5 domain profile. / tRNA synthetase B5 domain / Ferrodoxin-fold anticodon-binding domain / Ferrodoxin-fold anticodon-binding domain superfamily / Ferredoxin-fold anticodon binding domain / B3/4 domain / Ferredoxin-fold anticodon binding (FDX-ACB) domain profile. / Ferredoxin-fold anticodon binding domain / Phenylalanyl tRNA synthetase beta chain, core domain / Phenylalanyl tRNA synthetase beta chain CLM domain / Phenylalanine-tRNA ligase, class IIc, beta subunit / B3/B4 tRNA-binding domain / Phenylalanyl-tRNA synthetase-like, B3/B4 / 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
ADENOSINE-5'-[PHENYLALANINYL-PHOSPHATE] / : / Phenylalanine--tRNA ligase beta subunit / Phenylalanine--tRNA ligase alpha subunit
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsSafro, M.G. / Fishman, R. / Moor, N. / Ankilova, V.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure at 2.6 A resolution of phenylalanyl-tRNA synthetase complexed with phenylalanyl-adenylate in the presence of manganese.
Authors: Fishman, R. / Ankilova, V. / Moor, N. / Safro, M.
#1: Journal: Nat.Struct.Biol. / Year: 1995
Title: Structure pf phenylalanyl-tRNA synthetase from Thermus thermophilus
Authors: Mosyak, L. / Reshetnikova, L. / Goldgur, Y. / Delarue, M. / Safro, M.
#2: Journal: Structure / Year: 1997
Title: The crystal structure of phenylalanyl-tRNA synthetase from Thermus thermophilus complexed with cognate tRNA-Phe
Authors: Goldgur, Y. / Mosyak, L. / Reshetnikova, L. / Ankilova, V. / Khodyreva, S. / Safro, M.
#3: Journal: J.Mol.Biol. / Year: 1999
Title: Crystal Structures of phenylalnyl-tRNA synthetase complexed with phenylalanine and phenylalanyl-adenylate analogue
Authors: Reshenikova, L. / Moor, N. / Lavrik, O. / Vassyliev, D.
History
DepositionJul 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Aug 16, 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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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 / _struct_conn.pdbx_dist_value / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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: PHENYLALANYL-TRNA SYNTHETASE ALPHA CHAIN
B: PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,6755
Polymers126,0302
Non-polymers6453
Water5,206289
1
A: PHENYLALANYL-TRNA SYNTHETASE ALPHA CHAIN
B: PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN
hetero molecules

A: PHENYLALANYL-TRNA SYNTHETASE ALPHA CHAIN
B: PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,35110
Polymers252,0604
Non-polymers1,2916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area29280 Å2
ΔGint-165 kcal/mol
Surface area80120 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)173.400, 173.400, 138.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Cell settingtrigonal
Space group name H-MP3221
DetailsThe second part of the molecule is generated by the two fold axis: y,x,-z'

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Components

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PHENYLALANYL-TRNA SYNTHETASE ... , 2 types, 2 molecules AB

#1: Protein PHENYLALANYL-TRNA SYNTHETASE ALPHA CHAIN / E.C.6.1.1.20 / PHENYLALANINE--TRNA LIGASE ALPHA CHAIN / PHERS / phenylalanine--tRNA ligase


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: Q5SGX2, phenylalanine-tRNA ligase
#2: Protein PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN / E.C.6.1.1.20 / PHENYLALANINE--TRNA LIGASE BETA CHAIN / PHERS / phenylalanine--tRNA ligase


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: Q5SGX1, phenylalanine-tRNA ligase

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Non-polymers , 4 types, 292 molecules

#3: Chemical ChemComp-FA5 / ADENOSINE-5'-[PHENYLALANINYL-PHOSPHATE]


Type: RNA linking / Mass: 494.395 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N6O8P
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 4.76 Å3/Da / Density % sol: 74.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: (NH4)2SO4, Imidazole-HCl, ATP, L-phenylalanine, MnSO4, pH 7.8, VAPOR DIFFUSION, HANGING DROP at 277K
Crystal grow
*PLUS
Components of the solutions
*PLUS
Conc.: 27 %sat / Common name: ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.98 Å
DetectorType: BRANDEIS / Detector: CCD / Date: Feb 17, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 75189 / % possible obs: 94.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 15.8
Reflection
*PLUS
Num. measured all: 405589
Reflection shell
*PLUS
% possible obs: 81.7 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1PYS

1pys


Resolution: 2.6→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 6846 10 %Random
Rwork0.216 ---
all0.239 70750 --
obs0.207 68983 95.7 %-
Displacement parametersBiso mean: 45.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8250 0 40 289 8579
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.76
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.003
RfactorNum. reflection% reflection
Rfree0.37 1065 -
Rwork0.31 --
obs-9894 90 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 45.2 Å2
LS refinement shell
*PLUS
Rfactor Rfree: 0.37 / Rfactor Rwork: 0.31

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