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- PDB-5fon: Crystal structure of the Cryptosporidium muris cytosolic leucyl-t... -

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Basic information

Entry
Database: PDB / ID: 5fon
TitleCrystal structure of the Cryptosporidium muris cytosolic leucyl-tRNA synthetase editing domain (apo structure)
Components(LEUCYL-TRNA SYNTHETASE) x 2
KeywordsLIGASE / CRYPTOSPORIDIUM / LEUCINE-TRNA LIGASE (LEURS) ACTIVITY / ATP + L-LEUCINE + TRNA(LEUCINE) GIVE AMP + DIPHOSPHATE + L-LEUCYL-TRNA(LEUCINE) / POST-TRANSFER EDITING ACTIVITY OF LEURS / AMINOACYL-TRNA SYNTHETASE / PROTEIN BIOSYNTHESIS / NOVEL BORON INHIBITORS OF THE EDITING SITE OF LEURS
Function / homology
Function and homology information


leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding
Similarity search - Function
Leucyl-tRNA synthetase, class Ia, archaeal/eukaryotic cytosolic / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding / Anticodon-binding domain of tRNA ligase / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
leucine--tRNA ligase
Similarity search - Component
Biological speciesCRYPTOSPORIDIUM MURIS (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPalencia, A. / Liu, R.J. / Lukarska, M. / Gut, J. / Bougdour, A. / Touquet, B. / Wang, E.D. / Alley, M.R.K. / Rosenthal, P.J. / Hakimi, M.A. / Cusack, S.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2016
Title: Cryptosporidium and Toxoplasma Parasites are Inhibited by a Benzoxaborole Targeting Leucyl-tRNA Synthetase.
Authors: Palencia, A. / Liu, R. / Lukarska, M. / Gut, J. / Bougdour, A. / Touquet, B. / Wang, E. / Li, X. / Alley, M.R.K. / Freund, Y.R. / Rosenthal, P.J. / Hakimi, M. / Cusack, S.
History
DepositionNov 24, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Oct 5, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LEUCYL-TRNA SYNTHETASE
B: LEUCYL-TRNA SYNTHETASE
C: LEUCYL-TRNA SYNTHETASE
D: LEUCYL-TRNA SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)131,6794
Polymers131,6794
Non-polymers00
Water1,27971
1
A: LEUCYL-TRNA SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)32,9161
Polymers32,9161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LEUCYL-TRNA SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)32,9301
Polymers32,9301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: LEUCYL-TRNA SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)32,9161
Polymers32,9161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: LEUCYL-TRNA SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)32,9161
Polymers32,9161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.708, 107.708, 311.199
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein LEUCYL-TRNA SYNTHETASE /


Mass: 32916.227 Da / Num. of mol.: 3 / Fragment: EDITING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CRYPTOSPORIDIUM MURIS (eukaryote) / Strain: RN66 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: B6AA20, leucine-tRNA ligase
#2: Protein LEUCYL-TRNA SYNTHETASE /


Mass: 32930.254 Da / Num. of mol.: 1 / Fragment: EDITING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CRYPTOSPORIDIUM MURIS (eukaryote) / Strain: RN66 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: B6AA20, leucine-tRNA ligase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 3.4 Å3/Da / Density % sol: 64 % / Description: NONE
Crystal growpH: 6.8
Details: 0.1 M MES (PH 6.8), 2% ETHANOL AND 10% (W/V) PEG 20000. 20% (V/V) ETHYLENE GLYCOL WAS USED AS CRYOPROTECTANT.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.7→48 Å / Num. obs: 51501 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 8.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 30
Reflection shellResolution: 2.7→2.84 Å / Redundancy: 9 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 2.7 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WFG

2wfg


Resolution: 2.7→48 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / SU B: 26.826 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R: 0.443 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.25561 2609 5.1 %RANDOM
Rwork0.20303 ---
obs0.20563 48772 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 90.569 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2--0.67 Å20 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8659 0 0 71 8730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.028837
X-RAY DIFFRACTIONr_bond_other_d0.0020.028627
X-RAY DIFFRACTIONr_angle_refined_deg1.841211936
X-RAY DIFFRACTIONr_angle_other_deg1.047320015
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.56251072
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.33824.833360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.132151657
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6811533
X-RAY DIFFRACTIONr_chiral_restr0.10.21345
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219608
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021795
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1785.6074321
X-RAY DIFFRACTIONr_mcbond_other3.1795.6064320
X-RAY DIFFRACTIONr_mcangle_it5.038.3965382
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2636.0184515
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.698→2.768 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 204 -
Rwork0.344 3508 -
obs--99.04 %
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)
10.8359-0.51550.26213.25310.40082.4465-0.0280.01180.0281-0.3568-0.04440.2444-0.0252-0.36040.07240.1970.0289-0.10030.27650.00160.05957.7127.718-43.643
21.43440.103-0.2022.04240.34632.3270.1813-0.18030.13320.17920.0545-0.1815-0.0935-0.1481-0.23580.2970.1044-0.08550.1968-0.08360.09125.36448.241-14.198
33.0815-0.34190.09340.676-0.66344.2755-0.3894-0.2376-0.2360.41050.52530.0204-1.1898-0.4037-0.13590.68340.37720.16230.42450.04760.067-26.26258.966-26.603
43.0108-0.05650.8242.96490.3732.0923-0.01580.2518-0.0578-0.23890.0554-0.30050.02250.3077-0.03960.4915-0.0379-0.00950.11450.05920.1275-8.38479.102-53.825
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D255 - 541
2X-RAY DIFFRACTION2A255 - 541
3X-RAY DIFFRACTION3B255 - 541
4X-RAY DIFFRACTION4C256 - 541

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