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- PDB-2akw: Crystal Structure of T.Thermophilus Phenylalanyl-tRNA synthetase ... -

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Basic information

Entry
Database: PDB / ID: 2akw
TitleCrystal Structure of T.Thermophilus Phenylalanyl-tRNA synthetase complexed with p-Cl-Phenylalanine
Components(Phenylalanyl-tRNA synthetase ...) x 2
KeywordsLIGASE / protein-unnatural amino acid complex
Function / homology
Function and homology information


phenylalanine-tRNA ligase complex / 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
4-CHLORO-L-PHENYLALANINE / : / Phenylalanine--tRNA ligase alpha subunit / Phenylalanine--tRNA ligase beta subunit / Phenylalanine--tRNA ligase beta subunit
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.8 Å
AuthorsKotik-Kogan, O.M. / Moor, N.A. / Tworowski, D.E. / Safro, M.G.
CitationJournal: Structure / Year: 2005
Title: Structural Basis for Discrimination of L-Phenylalanine from L-Tyrosine by Phenylalanyl-tRNA Synthetase
Authors: Kotik-Kogan, O.M. / Moor, N.A. / Tworowski, D.E. / Safro, M.G.
History
DepositionAug 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Aug 23, 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: Phenylalanyl-tRNA synthetase alpha chain
B: Phenylalanyl-tRNA synthetase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,0275
Polymers116,6762
Non-polymers3513
Water3,549197
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)234,05310
Polymers233,3524
Non-polymers7016
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area27130 Å2
ΔGint-142 kcal/mol
Surface area78400 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)172.980, 172.980, 138.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Cell settingtrigonal
Space group name H-MP3221
DetailsThe biological assembly is a heterodimer generated from the dimer in the asymmetric unit by hte operations : 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


Mass: 29955.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: gene pheS / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P27001, phenylalanine-tRNA ligase
#2: Protein Phenylalanyl-tRNA synthetase beta chain / E.C.6.1.1.20 / Phenylalanine--tRNA ligase beta chain / PheRS


Mass: 86720.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: gene pheT / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
References: UniProt: P27002, UniProt: Q5SGX1*PLUS, phenylalanine-tRNA ligase

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Non-polymers , 4 types, 200 molecules

#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-200 / 4-CHLORO-L-PHENYLALANINE


Type: L-peptide linking / Mass: 199.634 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10ClNO2
#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.: 197 / 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: 5.17 Å3/Da / Density % sol: 76.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 20mM Imidazole-HCl (pH 7.2), 27% (NH4)2SO4, 1mM MgCl2, 1mM NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 60263 / Num. obs: 58657 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 41.9 Å2
Reflection shellResolution: 2.8→2.97 Å / % possible all: 99.9

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Processing

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

1pys


Resolution: 2.8→9.99 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2329075.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2896 5 %RANDOM
Rwork0.229 ---
all0.265 60263 --
obs0.262 58657 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.42 Å2 / ksol: 0.389 e/Å3
Displacement parametersBiso mean: 49.5 Å2
Baniso -1Baniso -2Baniso -3
1-6.74 Å213.06 Å20 Å2
2--6.74 Å20 Å2
3----13.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.8→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8250 0 19 197 8466
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d1.09
X-RAY DIFFRACTIONc_mcbond_it1.531.5
X-RAY DIFFRACTIONc_mcangle_it2.352
X-RAY DIFFRACTIONc_scbond_it2.552
X-RAY DIFFRACTIONc_scangle_it3.682.5
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.347 504 5.3 %
Rwork0.341 9002 -
all-9506 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.topprotein_rep.param
X-RAY DIFFRACTION2water.topwater_rep.param
X-RAY DIFFRACTION3fcl.topfcl.par
X-RAY DIFFRACTION4ion.topion.param

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