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- PDB-2wfg: Structure of the Candida albicans cytosolic leucyl-tRNA synthetas... -

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Basic information

Entry
Database: PDB / ID: 2wfg
TitleStructure of the Candida albicans cytosolic leucyl-tRNA synthetase editing domain bound to a benzoxaborole-AMP adduct
ComponentsCYTOSOLIC LEUCYL-TRNA SYNTHETASE
KeywordsLIGASE / LEUCYL-TRNA SYNTHETASE / EDITING DOMAIN / CANDIDA ALBICANS / HYDROLYSIS OF MIS-CHARGED TRNAS / BENZOXABOROLE / ANTI-FUNGAL
Function / homologyIsoleucyl-tRNA Synthetase; domain 2 / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Alpha-Beta Complex / Alpha Beta / Chem-ZZB / :
Function and homology information
Biological speciesCANDIDA ALBICANS (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSeiradake, E. / Mao, W. / Hernandez, V. / Baker, S.J. / Plattner, J.J. / Alley, M.R.K. / Cusack, S.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal Structures of the Human and Fungal Cytosolic Leucyl-tRNA Synthetase Editing Domains: A Structural Basis for the Rational Design of Antifungal Benzoxaboroles.
Authors: Seiradake, E. / Mao, W. / Hernandez, V. / Baker, S.J. / Plattner, J.J. / Alley, M.R.K. / Cusack, S.
History
DepositionApr 5, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOSOLIC LEUCYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0202
Polymers29,4971
Non-polymers5231
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)43.020, 58.040, 97.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CYTOSOLIC LEUCYL-TRNA SYNTHETASE


Mass: 29496.615 Da / Num. of mol.: 1 / Fragment: EDITING OR CP1 DOMAIN, RESIDUES 280-530
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CANDIDA ALBICANS (yeast) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH10B / Variant (production host): 10G / References: UniProt: Q5A9A4
#2: Chemical ChemComp-ZZB / [(1S,3S,5R,6R,8R)-6-(6-AMINOPURIN-9-YL)-4'-ETHYLAMINO-3'-FLUORO-SPIRO[2,4,7-TRIOXA-3-BORANUIDABICYCLO[3.3.0]OCTANE-3,7'-8-OXA-7-BORANUIDABICYCLO[4.3.0]NONA-1,3,5-TRIENE]-8-YL]METHYL DIHYDROGEN PHOSPHATE


Mass: 523.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22BFN6O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsAN3018-AMP ADDUCT (ZZB): AN3018 IS 6-ETHYLAMINO-5-FLUOROBENZO-C-1,2-OXABOROL-1-3H-OL

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 41.1 % / Description: NONE
Crystal growDetails: 0.2 M SODIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 6.5, 30 % PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 12930 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.49 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 8.16
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 3.31 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.26 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→49.88 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.883 / SU B: 16.747 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.343 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26155 629 4.9 %RANDOM
Rwork0.1845 ---
obs0.18811 12300 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2---0.87 Å20 Å2
3---0.79 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1974 0 36 247 2257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222056
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1532.0042792
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8355249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.93225.28189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.38915358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.994157
X-RAY DIFFRACTIONr_chiral_restr0.0740.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211538
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.4191.51244
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.78222019
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.1073812
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8544.5773
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: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 48 -
Rwork0.288 902 -
obs--99.48 %
Refinement TLS params.Method: refined / Origin x: 11.37 Å / Origin y: 2.259 Å / Origin z: 11.672 Å
111213212223313233
T0.0665 Å20.0008 Å2-0.0113 Å2-0.0314 Å2-0.0031 Å2--0.0356 Å2
L1.7707 °2-0.0712 °2-0.488 °2-1.3608 °20.3176 °2--1.1226 °2
S-0.0004 Å °-0.0897 Å °0.0013 Å °0.0403 Å °-0.0373 Å °0.0449 Å °0.0397 Å °-0.0477 Å °0.0378 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A279 - 528
2X-RAY DIFFRACTION1A1529

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