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- PDB-6c86: Crystal Structure of Lysyl-tRNA Synthetase from Cryptosporidium p... -

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Basic information

Entry
Database: PDB / ID: 6c86
TitleCrystal Structure of Lysyl-tRNA Synthetase from Cryptosporidium parvum complexed with L-Lysylsulfamoyl Adenosine
ComponentsLysine--tRNA ligase
KeywordsLIGASE / SSGCID / Lysine--tRNA ligase / Cryptosporidium parvum / ATP binding / aminoacylation / 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
5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE / Lysine--tRNA ligase
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 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-Lysylsulfamoyl Adenosine
Authors: Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJan 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 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)124,46213
Polymers122,9182
Non-polymers1,54411
Water15,187843
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11690 Å2
ΔGint-72 kcal/mol
Surface area38590 Å2
MethodPISA
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)248,92426
Polymers245,8364
Non-polymers3,08822
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area26200 Å2
ΔGint-184 kcal/mol
Surface area74720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.030, 142.870, 73.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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, 854 molecules

#2: Chemical ChemComp-KAA / 5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE / 5'-O-[N-(L-LYSYL)SULFAMOYL]ADENOSINE


Mass: 474.492 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H26N8O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 843 / 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: 50.62 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: CrpaA.00612.a.A3.PW37710 @35 mg/ml, protein was incubated with 3 mM L-Lysylsulfamoyl Adenosine, then mixed 1:1 with IndexG5opt(g3): 23.41% (w/v) PEG-3350, 0.2 M lithium sulfate, 0.1 M Tris: ...Details: CrpaA.00612.a.A3.PW37710 @35 mg/ml, protein was incubated with 3 mM L-Lysylsulfamoyl Adenosine, then mixed 1:1 with IndexG5opt(g3): 23.41% (w/v) PEG-3350, 0.2 M lithium sulfate, 0.1 M Tris:HCl/NaOH, pH = 7.7: cryoprotected with 20% ethylene glycol. Puck: yoz9-1, tray: 297540g3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 12, 2018
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.15→46.86 Å / Num. obs: 67507 / % possible obs: 100 % / Redundancy: 6.519 % / Biso Wilson estimate: 31.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rrim(I) all: 0.102 / Χ2: 1.01 / Net I/σ(I): 12.64 / Num. measured all: 440089
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.15-2.216.3050.573.2949650.8630.622100
2.21-2.276.6270.4893.9647820.920.531100
2.27-2.336.5330.424.4846600.9230.457100
2.33-2.46.5320.3635.1145430.9420.395100
2.4-2.486.7950.3195.9243890.9620.346100
2.48-2.576.6660.2626.9142920.9740.285100
2.57-2.676.3980.2257.7241060.9780.245100
2.67-2.786.7570.1939.0639770.9850.20999.9
2.78-2.96.4670.15810.5738240.9890.173100
2.9-3.046.7060.12912.936770.9920.14100
3.04-3.216.7310.10415.4134880.9950.113100
3.21-3.46.3660.08718.0732850.9950.095100
3.4-3.636.6020.07221.731280.9970.07999.9
3.63-3.936.2660.06423.829060.9970.06999.9
3.93-4.36.6430.05626.3126970.9980.061100
4.3-4.816.260.05227.3724310.9980.057100
4.81-5.556.3890.05426.5221770.9980.059100
5.55-6.86.2880.05425.218550.9980.059100
6.8-9.626.1320.04629.1614590.9980.0599.7
9.62-46.865.90.03732.338660.9990.0498.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ELO

5elo


Resolution: 2.15→46.86 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.88
RfactorNum. reflection% reflection
Rfree0.2039 1977 2.93 %
Rwork0.1549 --
obs0.1563 67498 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 139.28 Å2 / Biso mean: 35.8385 Å2 / Biso min: 16.07 Å2
Refinement stepCycle: final / Resolution: 2.15→46.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7958 0 97 850 8905
Biso mean--41.96 40.83 -
Num. residues----998
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.15-2.20380.25641400.194646364776
2.2038-2.26330.23021540.180545804734
2.2633-2.32990.25141460.176246024748
2.3299-2.40510.23641530.174846314784
2.4051-2.49110.24181290.168546344763
2.4911-2.59080.21841430.164346434786
2.5908-2.70870.23421660.163546254791
2.7087-2.85150.22741460.169446204766
2.8515-3.03010.21321180.165546964814
3.0301-3.26410.21971430.166146634806
3.2641-3.59240.20841300.154147024832
3.5924-4.1120.19151370.138347344871
4.112-5.17960.1511330.121147854918
5.1796-46.87110.17591390.158549705109
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)
12.332-1.1214-0.84822.37330.18522.2218-0.1056-0.2846-0.24380.11830.0280.18840.03240.03430.0610.2455-0.0459-0.00890.25380.0280.2222-42.526513.8373-12.9683
20.91780.0492-0.23590.75820.1140.66820.0077-0.0592-0.09130.0332-0.0126-0.1340.01350.0890.00310.21510.0029-0.00880.1850.0050.1942-5.986221.8311-43.9307
31.26860.7989-0.68692.5575-1.12312.6005-0.05110.24070.0276-0.16190.09320.0629-0.2094-0.1952-0.02040.30320.0215-0.01140.34950.010.1733-13.242532.632-74.5213
40.6160.115-0.05150.5168-0.180.487-0.03090.0897-0.1521-0.0450.03970.01260.0857-0.1279-0.01230.2013-0.01340.00280.2588-0.01430.2545-37.33212.7406-43.9208
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 45 through 209 )A45 - 209
2X-RAY DIFFRACTION2chain 'A' and (resid 210 through 545 )A210 - 545
3X-RAY DIFFRACTION3chain 'B' and (resid 45 through 209 )B45 - 209
4X-RAY DIFFRACTION4chain 'B' and (resid 210 through 545 )B210 - 545

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