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- PDB-4tqd: Crystal Structure of the C-terminal domain of IFRS bound with 3-i... -

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Basic information

Entry
Database: PDB / ID: 4tqd
TitleCrystal Structure of the C-terminal domain of IFRS bound with 3-iodo-L-Phe and ATP
ComponentsPyrrolysine--tRNA ligase
KeywordsLIGASE / Amino Acyl-tRNA Synthetases / Archaeal Proteins / Evolution / Molecular / Genetic Code / Substrate Specificity
Function / homology
Function and homology information


pyrrolysine-tRNAPyl ligase / pyrrolysyl-tRNA synthetase activity / tRNA aminoacylation for protein translation / tRNA binding / ATP binding / cytoplasm
Similarity search - Function
Pyrrolysyl-tRNA ligase / Pyrrolysyl-tRNA ligase, N-terminal / Helix hairpin bin / Pyrrolysyl-tRNA ligase, C-terminal / Phenylalanyl-tRNA synthetase / tRNA synthetases class II core domain (F) / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. ...Pyrrolysyl-tRNA ligase / Pyrrolysyl-tRNA ligase, N-terminal / Helix hairpin bin / Pyrrolysyl-tRNA ligase, C-terminal / Phenylalanyl-tRNA synthetase / tRNA synthetases class II core domain (F) / 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) / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
3-iodo-L-phenylalanine / ADENOSINE-5'-TRIPHOSPHATE / Pyrrolysine--tRNA ligase
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1429 Å
AuthorsNakamura, A. / O'Donoghue, P. / Soll, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Polyspecific pyrrolysyl-tRNA synthetases from directed evolution.
Authors: Guo, L.T. / Wang, Y.S. / Nakamura, A. / Eiler, D. / Kavran, J.M. / Wong, M. / Kiessling, L.L. / Steitz, T.A. / O'Donoghue, P. / Soll, D.
History
DepositionJun 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Dec 3, 2014Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyrrolysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,70513
Polymers33,3991
Non-polymers1,30612
Water2,126118
1
A: Pyrrolysine--tRNA ligase
hetero molecules

A: Pyrrolysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,41026
Polymers66,7982
Non-polymers2,61124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area9830 Å2
ΔGint-28 kcal/mol
Surface area22620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.700, 104.700, 70.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Pyrrolysine--tRNA ligase / Pyrrolysine--tRNA(Pyl) ligase / Pyrrolysyl-tRNA synthetase / PylRS


Mass: 33399.219 Da / Num. of mol.: 1 / Mutation: N346S, C348I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea)
Strain: ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88
Gene: pylS, MM_1445 / Plasmid: pet15b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 Codon Plus RIL (DE3) / References: UniProt: Q8PWY1, pyrrolysine-tRNAPyl ligase

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Non-polymers , 5 types, 130 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-33S / 3-iodo-L-phenylalanine


Type: L-peptide linking / Mass: 291.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10INO2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 3.35 Å3/Da / Density % sol: 63.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Hepes, MgCl2, PEG3350 / PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.14→42.064 Å / Num. obs: 24274 / % possible obs: 99.8 % / Redundancy: 20 % / Net I/σ(I): 34.24

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZIM

2zim


Resolution: 2.1429→42.064 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 19.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1925 2433 10.02 %
Rwork0.1551 --
obs0.1589 24270 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1429→42.064 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2100 0 75 118 2293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142253
X-RAY DIFFRACTIONf_angle_d1.453029
X-RAY DIFFRACTIONf_dihedral_angle_d17.011894
X-RAY DIFFRACTIONf_chiral_restr0.069324
X-RAY DIFFRACTIONf_plane_restr0.007387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1429-2.18660.23081370.18371222X-RAY DIFFRACTION97
2.1866-2.23420.25711260.1781309X-RAY DIFFRACTION100
2.2342-2.28610.21411340.17991286X-RAY DIFFRACTION100
2.2861-2.34330.24481400.16691291X-RAY DIFFRACTION100
2.3433-2.40660.20781300.16021265X-RAY DIFFRACTION100
2.4066-2.47740.22051460.16841289X-RAY DIFFRACTION100
2.4774-2.55740.23811400.17331284X-RAY DIFFRACTION100
2.5574-2.64880.20591400.16351271X-RAY DIFFRACTION100
2.6488-2.75480.21571400.16911302X-RAY DIFFRACTION100
2.7548-2.88020.2181590.16591264X-RAY DIFFRACTION100
2.8802-3.0320.21251410.17041290X-RAY DIFFRACTION100
3.032-3.22190.22031420.17221275X-RAY DIFFRACTION100
3.2219-3.47050.23671610.17051279X-RAY DIFFRACTION100
3.4705-3.81960.20031370.15571307X-RAY DIFFRACTION100
3.8196-4.37180.14521560.13291283X-RAY DIFFRACTION100
4.3718-5.5060.16671500.12791302X-RAY DIFFRACTION100
5.506-42.07170.15091540.14981318X-RAY DIFFRACTION100

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