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- PDB-1b7y: PHENYLALANYL TRNA SYNTHETASE COMPLEXED WITH PHENYLALANINYL-ADENYLATE -

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Basic information

Entry
Database: PDB / ID: 1b7y
TitlePHENYLALANYL TRNA SYNTHETASE COMPLEXED WITH PHENYLALANINYL-ADENYLATE
Components(PROTEIN (PHENYLALANYL-TRNA SYNTHETASE)) x 2
KeywordsLIGASE / ENZYME / TRNA SYNTHETASE / ALPHA/BETA HOMODIMER
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
ADENOSINE-5'-[PHENYLALANINOL-PHOSPHATE] / Phenylalanine--tRNA ligase alpha subunit / Phenylalanine--tRNA ligase beta subunit
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsReshetnikova, L. / Moor, N. / Lavrik, O. / Vassylyev, D.G.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Crystal structures of phenylalanyl-tRNA synthetase complexed with phenylalanine and a phenylalanyl-adenylate analogue.
Authors: Reshetnikova, L. / Moor, N. / Lavrik, O. / Vassylyev, D.G.
#1: Journal: 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.
#2: Journal: Nature New Biol. / Year: 1995
Title: Structure of Phenylalanyl-tRNA Synthetase from Thermus Thermophilus
Authors: Mosyak, L. / Reshetnikova, L. / Goldgur, Y. / Delarue, M. / Safro, M.G.
History
DepositionJan 26, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 15, 2017Group: Database references
Revision 1.4Aug 9, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PROTEIN (PHENYLALANYL-TRNA SYNTHETASE)
B: PROTEIN (PHENYLALANYL-TRNA SYNTHETASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,5354
Polymers126,0302
Non-polymers5052
Water4,306239
1
A: PROTEIN (PHENYLALANYL-TRNA SYNTHETASE)
B: PROTEIN (PHENYLALANYL-TRNA SYNTHETASE)
hetero molecules

A: PROTEIN (PHENYLALANYL-TRNA SYNTHETASE)
B: PROTEIN (PHENYLALANYL-TRNA SYNTHETASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,0698
Polymers252,0604
Non-polymers1,0094
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area27750 Å2
ΔGint-134 kcal/mol
Surface area80190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.500, 174.500, 140.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Cell settingtrigonal
Space group name H-MP3221

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Components

#1: Protein PROTEIN (PHENYLALANYL-TRNA SYNTHETASE) / E.C.6.1.1.20 / PHERS


Mass: 39309.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Cellular location: CYTOPLASM / References: UniProt: P27001, phenylalanine-tRNA ligase
#2: Protein PROTEIN (PHENYLALANYL-TRNA SYNTHETASE) / EC 6.1.1.20 / PHERS


Mass: 86720.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Cellular location: CYTOPLASM / References: UniProt: P27002, phenylalanine-tRNA ligase
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-FYA / ADENOSINE-5'-[PHENYLALANINOL-PHOSPHATE]


Mass: 480.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H25N6O7P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 3.8 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 313 K / Method: vapor diffusion, hanging drop / pH: 7
Details: HANGING-DROP TECHNIQUE AT 4O C WITH (NH4)2SO4 AS PRECIPITANT. EACH DROPLET OF THE PHENYLALANYL-TRNA SYNTHETASE SOLUTION (10 microliters) AT PROTEIN CONCENTRATION OF 3 TO 5 MG PER ML IN 20 MM ...Details: HANGING-DROP TECHNIQUE AT 4O C WITH (NH4)2SO4 AS PRECIPITANT. EACH DROPLET OF THE PHENYLALANYL-TRNA SYNTHETASE SOLUTION (10 microliters) AT PROTEIN CONCENTRATION OF 3 TO 5 MG PER ML IN 20 MM IMIDASOL-HCL BUFFER (PH 7.8), 1 MM MGCL2, 1 MM NAN3 AND 15% SATURATED (NH4)2SO4 IN THE SAME BUFFER. CRYSTALS APPEARED AFTER ONE TO TWO WEEKS AND GREW UP TO THE MAXIMAL DIMENSIONS OF 0.4X0.4X0.25 MM IN A FEW WEEKS, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 313K
Components of the solutions
IDNameCrystal-IDSol-ID
1IMIDASOL-HCL11
2MGCL211
3NAN311
4(NH4)2SO411
5(NH4)2SO412
Crystal
*PLUS
Density % sol: 75 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.8 / Details: Chernaya, M., (1987) J. Mol. Biol., 198, 555.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13-5 mg/mlprotein1drop
220 mMimidazole-HCl1drop
31 mM1dropMgCl2
41 mM1dropNaN3
515 %satammonium sulfate1drop
625-30 %satammonium sulfate1reservoir
720 mMimidazole-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Dec 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 81613 / Num. obs: 81613 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 2.2 / % possible all: 88.5
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 88.5 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PYS

1pys


Resolution: 2.5→50 Å / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.267 4000 5 %RANDOM
Rwork0.23 ---
all-81613 --
obs-81613 95.7 %-
Displacement parametersBiso mean: 62 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8166 0 34 239 8439
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.72
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.83
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.71.5
X-RAY DIFFRACTIONx_mcangle_it5.22
X-RAY DIFFRACTIONx_scbond_it62
X-RAY DIFFRACTIONx_scangle_it8.52.5
LS refinement shellResolution: 2.5→2.61 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.43 453 5 %
Rwork0.41 8892 -
obs--88.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARNAH1E.DNATOPNAH1E.DNA
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.83

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