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- PDB-6bni: Crystal Structure of Lysyl-tRNA Synthetase from Cryptosporidium p... -

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Basic information

Entry
Database: PDB / ID: 6bni
TitleCrystal Structure of Lysyl-tRNA Synthetase from Cryptosporidium parvum complexed with L-lysine and Adenosine
ComponentsLysine--tRNA ligase
KeywordsLIGASE / SSGCID / Lysine--tRNA ligase / Cryptosporidium parvum / ATP binding / aminoacylation / cladosporin / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / nucleic acid binding / ATP binding / membrane / 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
ADENOSINE / LYSINE / Lysine--tRNA ligase
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Lysyl-tRNA Synthetase from Cryptosporidium parvum complexed with L-lysine and Adenosine
Authors: Dranow, D.M. / Lorimer, D. / Edwards, T.E.
History
DepositionNov 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_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)125,02924
Polymers122,9182
Non-polymers2,11122
Water19,4921082
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12600 Å2
ΔGint-91 kcal/mol
Surface area38900 Å2
2
A: Lysine--tRNA ligase
B: Lysine--tRNA ligase
hetero molecules

A: Lysine--tRNA ligase
B: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,05848
Polymers245,8364
Non-polymers4,22244
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area28040 Å2
ΔGint-218 kcal/mol
Surface area75350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.870, 142.630, 72.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 61459.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (strain Iowa II) (eukaryote)
Strain: Iowa II / Gene: cgd4_2370 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5CR27, lysine-tRNA ligase

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Non-polymers , 6 types, 1104 molecules

#2: Chemical ChemComp-LYS / LYSINE / Lysine


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Chemical ChemComp-ADN / ADENOSINE / Adenosine


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1082 / 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: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.89
Details: CrpaA.00612.a.A3.PW37710 at 35 mg/ml, protein was incubated with 4 mM L-lysine and 4 mM Adenosine, then mixed 1:1 with 26.14% (w/v) PEG-3350, 0.2 M lithium sulfate, 0.1 M Tris-HCl/NaOH, pH = ...Details: CrpaA.00612.a.A3.PW37710 at 35 mg/ml, protein was incubated with 4 mM L-lysine and 4 mM Adenosine, then mixed 1:1 with 26.14% (w/v) PEG-3350, 0.2 M lithium sulfate, 0.1 M Tris-HCl/NaOH, pH = 7.89. Crystals were cryoprotected with 20% ethylene glycol. Puck: pqf5-7, tray: 296117b9.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 2, 2017 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.85→46.792 Å / Num. obs: 105099 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.977 % / Biso Wilson estimate: 21.84 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 18
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 4.99 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 2.88 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ELO

5elo


Resolution: 1.85→46.79 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.84
RfactorNum. reflection% reflection
Rfree0.185 1947 1.85 %
Rwork0.152 --
obs0.153 105085 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 29.86 Å2
Refinement stepCycle: LAST / Resolution: 1.85→46.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8003 0 133 1082 9218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.89630.27021240.22617309X-RAY DIFFRACTION100
1.8963-1.94750.29991360.21037296X-RAY DIFFRACTION100
1.9475-2.00490.23321290.1967297X-RAY DIFFRACTION100
2.0049-2.06960.22041290.1747322X-RAY DIFFRACTION100
2.0696-2.14350.20951430.15917345X-RAY DIFFRACTION100
2.1435-2.22940.16251470.15147294X-RAY DIFFRACTION100
2.2294-2.33080.18391600.14927278X-RAY DIFFRACTION100
2.3308-2.45370.1851370.1547364X-RAY DIFFRACTION100
2.4537-2.60740.21261410.1567348X-RAY DIFFRACTION100
2.6074-2.80870.19391190.1617409X-RAY DIFFRACTION100
2.8087-3.09130.21761440.1627361X-RAY DIFFRACTION100
3.0913-3.53850.18061420.14557407X-RAY DIFFRACTION100
3.5385-4.45760.15091480.12367453X-RAY DIFFRACTION99
4.4576-46.80740.14871480.13937655X-RAY DIFFRACTION98
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)
11.2898-0.6217-0.30122.10720.1271.4948-0.1142-0.1609-0.16060.12370.05470.22350.0591-0.01080.05540.125-0.02540.00450.19070.03420.1604-43.120113.6562-12.8414
20.64870.0273-0.14930.66740.07280.50390.0104-0.0336-0.03010.0433-0-0.0760.02720.0269-0.01170.18390.0050.00190.17170.00530.1674-6.312821.764-43.5736
30.80310.6185-0.83330.6331-0.57411.546-0.00160.30010.0332-0.13190.080.0302-0.1462-0.206-0.05440.25360.0247-0.01140.27190.02290.1588-16.175831.2215-71.0708
40.48380.147-0.34830.4736-0.20860.8984-0.09960.0999-0.1222-0.14990.05550.01490.3357-0.17940.01680.263-0.07310.01270.1796-0.01820.1844-37.59321.1868-43.131
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 44 THROUGH 209 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 210 THROUGH 545 )
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID 44 THROUGH 232 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 233 THROUGH 546 )

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