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- PDB-1irx: Crystal structure of class I lysyl-tRNA synthetase -

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Basic information

Entry
Database: PDB / ID: 1irx
TitleCrystal structure of class I lysyl-tRNA synthetase
Componentslysyl-tRNA synthetase
KeywordsLIGASE / beta sandwitch / zinc-binding structure / Rossmann fold / alpha-helix cage / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / tRNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Arc Repressor Mutant, subunit A - #770 / class i lysyl-tRNA synthetase like / Lysine tRNA ligase, stem contact fold domain / Lysine-tRNA ligase / : / Lysine tRNA ligase, stem contact fold domain / tRNA synthetases class I (K) / Arc Repressor Mutant, subunit A - #350 / Aminoacyl-tRNA synthetase, class I, anticodon-binding domain, subdomain 2 / Anticodon binding domain ...Arc Repressor Mutant, subunit A - #770 / class i lysyl-tRNA synthetase like / Lysine tRNA ligase, stem contact fold domain / Lysine-tRNA ligase / : / Lysine tRNA ligase, stem contact fold domain / tRNA synthetases class I (K) / Arc Repressor Mutant, subunit A - #350 / Aminoacyl-tRNA synthetase, class I, anticodon-binding domain, subdomain 2 / Anticodon binding domain / Aminoacyl-tRNA synthetase, class I, anticodon-binding superfamily / Arc Repressor Mutant, subunit A / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Helix non-globular / Special / SH3 type barrels. / Arc Repressor Mutant, subunit A / Roll / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsNureki, O. / Terada, T. / Ishitani, R. / Ambrogelly, A. / Ibba, M. / Soll, D. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Functional convergence of two lysyl-tRNA synthetases with unrelated topologies.
Authors: Terada, T. / Nureki, O. / Ishitani, R. / Ambrogelly, A. / Ibba, M. / Soll, D. / Yokoyama, S.
History
DepositionOct 25, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_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_ref_seq_dif.details / _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: lysyl-tRNA synthetase
B: lysyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,5746
Polymers123,3132
Non-polymers2624
Water4,468248
1
A: lysyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7873
Polymers61,6561
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: lysyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7873
Polymers61,6561
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.945, 74.767, 156.945
Angle α, β, γ (deg.)90.00, 90.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein lysyl-tRNA synthetase


Mass: 61656.402 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: O57963, lysine-tRNA ligase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.8 Å3/Da / Density % sol: 56.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal
*PLUS
Density % sol: 56 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
2120 mMHEPES1reservoirpH7.5
32.4 Mammonium sulfate1reservoir
42.4 %(v/v)PEG4001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9792, 0.9795, 0.9824, 0.9724
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2001
RadiationMonochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97951
30.98241
40.97241
ReflectionResolution: 2.6→40 Å / Num. all: 41462 / Num. obs: 13821 / % possible obs: 93.1 % / Observed criterion σ(F): 2.6 / Observed criterion σ(I): 2.6 / Redundancy: 3 % / Rmerge(I) obs: 0.055
Reflection shellResolution: 2.6→2.62 Å / Mean I/σ(I) obs: 3.7 / Rsym value: 0.174 / % possible all: 76.2
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 40 Å / Num. obs: 41570 / % possible obs: 98.2 % / Redundancy: 3 % / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 76.2 % / Rmerge(I) obs: 0.174

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Processing

Software
NameVersionClassification
SHARPphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.6→40 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.292 2073 15 %random
Rwork0.225 ---
all0.247 41462 --
obs-13821 --
Refinement stepCycle: LAST / Resolution: 2.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8502 0 4 248 8754
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.24
X-RAY DIFFRACTIONc_dihedral_angle_d20.92
X-RAY DIFFRACTIONc_improper_angle_d0.78
Refinement
*PLUS
Lowest resolution: 40 Å / % reflection Rfree: 15 % / Rfactor all: 0.247 / Rfactor obs: 0.225 / Rfactor Rfree: 0.292 / Rfactor Rwork: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.24
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.92
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78

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