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

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Basic information

Entry
Database: PDB / ID: 5fom
TitleCrystal structure of the Cryptosporidium muris cytosolic leucyl-tRNA synthetase editing domain complex with the adduct AMP-AN6426
ComponentsLEUCYL-TRNA SYNTHETASE
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 deacylase 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
Chem-A2H / PHOSPHATE ION / leucine--tRNA ligase
Similarity search - Component
Biological speciesCRYPTOSPORIDIUM MURIS (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.3Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: LEUCYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5793
Polymers32,9161
Non-polymers6632
Water91951
1
A: LEUCYL-TRNA SYNTHETASE
hetero molecules

A: LEUCYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1586
Polymers65,8322
Non-polymers1,3254
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area4850 Å2
ΔGint-27 kcal/mol
Surface area23310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.065, 65.065, 167.301
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein LEUCYL-TRNA SYNTHETASE


Mass: 32916.227 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
#2: Chemical ChemComp-A2H / 4-Chloro-3-aminomethyl-7-[ethoxy]-3H-benzo[C][1,2]oxaborol-1-ol modified adenosine


Mass: 567.661 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22BClN6O9P
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 5.5
Details: 1.4 M SODIUM/POTASSIUM PHOSPHATE PH 5.5. 20% GLYCEROL 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: 2.1→60.64 Å / Num. obs: 21974 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 29
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 5.6 / % 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: 2.1→60.64 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 6.146 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23866 1122 5.1 %RANDOM
Rwork0.19941 ---
obs0.20135 20768 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.59 Å20 Å20 Å2
2--3.59 Å20 Å2
3----7.18 Å2
Refinement stepCycle: LAST / Resolution: 2.1→60.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2189 0 43 51 2283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022281
X-RAY DIFFRACTIONr_bond_other_d0.0020.022203
X-RAY DIFFRACTIONr_angle_refined_deg1.6672.0233089
X-RAY DIFFRACTIONr_angle_other_deg0.92735110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3835272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74124.78392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.27815421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.893159
X-RAY DIFFRACTIONr_chiral_restr0.1280.2343
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212462
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02466
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_it3.0425.2671094
X-RAY DIFFRACTIONr_mcbond_other3.0355.2671093
X-RAY DIFFRACTIONr_mcangle_it4.3647.8881364
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7235.7341187
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: 2.096→2.151 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 94 -
Rwork0.315 1444 -
obs--98.59 %

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