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- PDB-4ex5: Crystal structure of lysyl-tRNA synthetase LysRS from Burkholderi... -

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Basic information

Entry
Database: PDB / ID: 4ex5
TitleCrystal structure of lysyl-tRNA synthetase LysRS from Burkholderia thailandensis bound to lysine
ComponentsLysine--tRNA ligase
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / aminoacyl-tRNA synthetase / lysine tRNA ligase / protein synthesis / ATP-depenedent / tRNAlys / class IIb tRNA synthetase
Function / homology
Function and homology information


lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / tRNA binding / magnesium ion binding / ATP binding / cytosol
Similarity search - Function
Lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / 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 ...Lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / 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
LYSINE / Lysine--tRNA ligase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Sci Rep / Year: 2017
Title: Ligand co-crystallization of aminoacyl-tRNA synthetases from infectious disease organisms.
Authors: Moen, S.O. / Edwards, T.E. / Dranow, D.M. / Clifton, M.C. / Sankaran, B. / Van Voorhis, W.C. / Sharma, A. / Manoil, C. / Staker, B.L. / Myler, P.J. / Lorimer, D.D.
History
DepositionApr 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Mar 29, 2017Group: Database references
Revision 1.3Sep 13, 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_ncs_dom_lim / 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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_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: Lysine--tRNA ligase
B: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,4754
Polymers119,1812
Non-polymers2942
Water8,305461
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8760 Å2
ΔGint-30 kcal/mol
Surface area37970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.220, 118.540, 94.540
Angle α, β, γ (deg.)90.000, 113.230, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 15 - 601 / Label seq-ID: 36

Dom-IDAuth asym-IDLabel asym-ID
1AA - C
2BB - D

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Components

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


Mass: 59590.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / Gene: BTH_I1883, lysS / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2SXD6, lysine-tRNA ligase
#2: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 3.73 Å3/Da / Density % sol: 66.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: ButhA.00612.a.A1 PS01208 at 18.9 mg/mL against Morpheus H5, 10% PEG 20,000, 20% PEG 550 MME, 0.1 M MOPS/Hepes, 20 mM glutamate, 20 mM alanine, 20 mM glycine, 20 mM serine, 20 mM lysine, ...Details: ButhA.00612.a.A1 PS01208 at 18.9 mg/mL against Morpheus H5, 10% PEG 20,000, 20% PEG 550 MME, 0.1 M MOPS/Hepes, 20 mM glutamate, 20 mM alanine, 20 mM glycine, 20 mM serine, 20 mM lysine, crystal tracking ID 232983h5, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 68404 / Num. obs: 67117 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 39.185 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.87
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.4-2.460.4682.2711805482196.1
2.46-2.530.382.8912805484998.8
2.53-2.60.323.4512720475399.4
2.6-2.680.283.8212502459599.2
2.68-2.770.244.4712459449999.5
2.77-2.870.2045.3412272433999.4
2.87-2.980.1626.6111884414099
2.98-3.10.147.5211513400499.3
3.1-3.240.1079.411117384999.1
3.24-3.390.09110.6210586366499
3.39-3.580.09710.369959346697.7
3.58-3.790.0617.429376326397.8
3.79-4.060.05916.088884306397.5
4.06-4.380.03923.228268284997.1
4.38-4.80.03426.447614262897.2
4.8-5.370.03625.087025238497.3
5.37-6.20.04421.076293210996.6
6.2-7.590.03923.325228175196.6
7.59-10.730.02633.394095136393.9
10.730.02536.89212972889.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å45.76 Å
Translation3 Å45.76 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1bbu

1bbu


Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.2906 / WRfactor Rwork: 0.2532 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.739 / SU B: 10.223 / SU ML: 0.125 / SU R Cruickshank DPI: 0.3455 / SU Rfree: 0.2829 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2228 3401 5.1 %RANDOM
Rwork0.1892 ---
obs0.1909 67095 98.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.17 Å2 / Biso mean: 32.9777 Å2 / Biso min: 9.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20.86 Å2
2---1.21 Å20 Å2
3---1.58 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7588 0 20 461 8069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0197788
X-RAY DIFFRACTIONr_bond_other_d0.0040.025312
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.96410562
X-RAY DIFFRACTIONr_angle_other_deg1.103312841
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0035974
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.82623.298379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.361151272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5921573
X-RAY DIFFRACTIONr_chiral_restr0.0830.21173
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218798
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021683
Refine LS restraints NCS

Ens-ID: 1 / Number: 17714 / Refine-ID: X-RAY DIFFRACTION / Rms: 0.09 / Type: LOCAL / Weight: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 248 -
Rwork0.281 4478 -
all-4726 -
obs--96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.23150.2781-0.02690.5922-0.160.15090.01860.0104-0.0763-0.0269-0.0265-0.0649-0.01280.01230.00790.02780.0054-0.00320.038-0.01440.0732-21.806616.5059-6.5028
20.60670.2293-0.14410.4998-0.05010.03690.0834-0.05650.01390.1663-0.0873-0.0171-0.02550.01170.00390.0969-0.0566-0.02170.0579-0.0050.0212-23.95131.230512.4408
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 506
2X-RAY DIFFRACTION1A601
3X-RAY DIFFRACTION1A701 - 958
4X-RAY DIFFRACTION2B14 - 506
5X-RAY DIFFRACTION2B601
6X-RAY DIFFRACTION2B701 - 903

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