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- PDB-1pys: PHENYLALANYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS -

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Basic information

Entry
Database: PDB / ID: 1pys
TitlePHENYLALANYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS
Components(PHENYLALANYL-TRNA SYNTHETASE) x 2
KeywordsAMINOACYL-TRNA SYNTHETASE / PHENYLALANYL-TRNA SYNTHETASE / CLASS II AMINOACYL-TRNA SYNTHETASE / THERMUS THERMOPHILUS / RBD DOMAIN / SH3 DOMAIN / HELIX-TURN-HELIX MOTIF
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
Phenylalanine--tRNA ligase beta subunit / Phenylalanine--tRNA ligase alpha subunit
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.9 Å
AuthorsSafro, M. / Mosyak, L. / Goldgur, Y. / Reshetnikova, L. / Delarue, M.
CitationJournal: Nat.Struct.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
DepositionNov 14, 1996Processing site: BNL
Revision 1.0Nov 19, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _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.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_asym_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
B: PHENYLALANYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,0543
Polymers126,0302
Non-polymers241
Water5,981332
1
A: PHENYLALANYL-TRNA SYNTHETASE
B: PHENYLALANYL-TRNA SYNTHETASE
hetero molecules

A: PHENYLALANYL-TRNA SYNTHETASE
B: PHENYLALANYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,1086
Polymers252,0604
Non-polymers492
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area26850 Å2
ΔGint-144 kcal/mol
Surface area80340 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)176.000, 176.000, 141.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein PHENYLALANYL-TRNA SYNTHETASE


Mass: 39309.199 Da / Num. of mol.: 1 / 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


Mass: 86720.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SGX1, phenylalanine-tRNA ligase
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 4

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Sample preparation

CrystalDensity Matthews: 4.8 Å3/Da / Density % sol: 75 %
Crystal growTemperature: 277 K / pH: 7.7
Details: PROTEIN WAS CRYSTALLIZED FROM AMMONIUM SULFATE 28% OF SATURATION, 20 MM IMIDAZOLE, PH 7.7, 10 MM MGCL2, 1 MM NAN3 AT 4 DEGREES CELSIUS, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / 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: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Type: LURE / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1992 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.9→28 Å / Num. obs: 52260 / % possible obs: 92.9 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 59 Å2 / Rsym value: 0.084 / Net I/σ(I): 13.1
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 2.33 % / Mean I/σ(I) obs: 3 / Rsym value: 0.36 / % possible all: 75.2

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2.9→10 Å / Rfactor Rfree error: 0.0033 / Data cutoff high absF: 100000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.236 5119 10 %RANDOM
Rwork0.177 ---
obs0.177 50958 92 %-
Refine analyzeLuzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 2.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8250 0 1 332 8583
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
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_d25.44
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.524
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 2.9→3.03 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3309 499 10 %
Rwork0.2625 4231 -
obs--92.76 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOL
X-RAY DIFFRACTION3PARAM.MG
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 50589
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.441
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.524

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