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- PDB-3a74: Lysyl-tRNA synthetase from Bacillus stearothermophilus complexed ... -

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Basic information

Entry
Database: PDB / ID: 3a74
TitleLysyl-tRNA synthetase from Bacillus stearothermophilus complexed with Diadenosine Tetraphosphate (AP4A)
ComponentsLysyl-tRNA synthetase
KeywordsLIGASE / aminoacyl tRNA synthetase / PROTEIN BIOSYNTHESIS / Aminoacyl-tRNA synthetase / ATP-binding / Magnesium / Metal-binding / Nucleotide-binding
Function / homology
Function and homology information


lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / transferase activity / nucleic acid binding / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysine-tRNA ligase, class II / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 ...Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysine-tRNA ligase, class II / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
BIS(ADENOSINE)-5'-TETRAPHOSPHATE / 2,6-DIAMINO-HEXANOIC ACID AMIDE / Lysine--tRNA ligase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSakurama, H. / Takita, T. / Mikami, B. / Itoh, T. / Yasukawa, K. / Inouye, K.
CitationJournal: To be Published
Title: Crystal Structure of Lysyl-tRNA Synthetase from Bacillus stearothermophilus in Complex with Diadenosine Tetraphosphate (AP4A): Insights into AP4A Synthesis Mechanisms and Implication for ...Title: Crystal Structure of Lysyl-tRNA Synthetase from Bacillus stearothermophilus in Complex with Diadenosine Tetraphosphate (AP4A): Insights into AP4A Synthesis Mechanisms and Implication for Recognition of Discriminator Base of tRNA^Lys
Authors: Sakurama, H. / Takita, T. / Mikami, B. / Itoh, T. / Yasukawa, K. / Inouye, K.
History
DepositionSep 13, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: 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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_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
C: Lysyl-tRNA synthetase
D: Lysyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,65924
Polymers229,4374
Non-polymers4,22220
Water14,628812
1
A: Lysyl-tRNA synthetase
B: Lysyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,83012
Polymers114,7192
Non-polymers2,11110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8570 Å2
ΔGint-39 kcal/mol
Surface area38530 Å2
MethodPISA
2
C: Lysyl-tRNA synthetase
D: Lysyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,83012
Polymers114,7192
Non-polymers2,11110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8570 Å2
ΔGint-39 kcal/mol
Surface area38540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.176, 85.080, 151.764
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Lysyl-tRNA synthetase / Lysine--tRNA ligase / LysRS


Mass: 57359.305 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: lysS / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RHV9, lysine-tRNA ligase
#2: Chemical
ChemComp-B4P / BIS(ADENOSINE)-5'-TETRAPHOSPHATE / Ap4A


Mass: 836.387 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H28N10O19P4
#3: Chemical
ChemComp-LYN / 2,6-DIAMINO-HEXANOIC ACID AMIDE


Type: L-peptide linking / Mass: 146.211 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H16N3O
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 812 / 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: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 18% PEG4000, 0.2M PIPES, 1.0M LiCl, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 27, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 554006 / Num. obs: 185105 / Biso Wilson estimate: 13.8 Å2 / Rsym value: 0.0049

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Processing

Software
NameClassification
DENZOdata reduction
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→14.96 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2688100.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.228 18367 10 %RANDOM
Rwork0.207 ---
obs0.207 183643 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.2754 Å2 / ksol: 0.394726 e/Å3
Displacement parametersBiso mean: 19 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å20 Å20 Å2
2--2.06 Å20 Å2
3----0.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.8→14.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15824 0 264 812 16900
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.251 2998 9.9 %
Rwork0.226 27172 -
obs--96.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4cis_peptide.paramAP4A.top
X-RAY DIFFRACTION5AP4A_AMD.param

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