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- PDB-5agj: Crystal structure of the LeuRS editing domain of Candida albicans... -

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Basic information

Entry
Database: PDB / ID: 5agj
TitleCrystal structure of the LeuRS editing domain of Candida albicans in complex with the adduct AN2690-AMP
ComponentsPOTENTIAL CYTOSOLIC LEUCYL TRNA SYNTHETASE
KeywordsLIGASE / AMINOACYL-TRNA SYNTHETASE / AMINOACYLATION / PROTEIN SYNTHESIS / PROOF-READING MECHANISMS / ANTIFUNGAL TARGET
Function / homologyIsoleucyl-tRNA Synthetase; domain 2 / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Alpha-Beta Complex / Alpha Beta / Chem-ANZ / :
Function and homology information
Biological speciesCANDIDA ALBICANS (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhao, H. / Palencia, A. / Seiradake, E. / Ghaemi, Z. / Luthey-Schulten, Z. / Cusack, S. / Martinis, S.A.
CitationJournal: Acs Chem.Biol. / Year: 2015
Title: Analysis of the Resistance Mechanism of a Benzoxaborole Inhibitor Reveals Insight Into the Leucyl-tRNA Synthetase Editing Mechanism.
Authors: Zhao, H. / Palencia, A. / Seiradake, E. / Ghaemi, Z. / Cusack, S. / Luthey-Schulten, Z. / Martinis, S.
History
DepositionFeb 2, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Oct 28, 2015Group: Database references
Revision 1.3Jan 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

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Assembly

Deposited unit
A: POTENTIAL CYTOSOLIC LEUCYL TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9782
Polymers29,4981
Non-polymers4801
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.950, 59.260, 97.150
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 POTENTIAL CYTOSOLIC LEUCYL TRNA SYNTHETASE


Mass: 29497.600 Da / Num. of mol.: 1 / Fragment: EDITING DOMAIN (CP1), UNP RESIDUES 280-530
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CANDIDA ALBICANS (yeast) / Strain: SC5314 / Production host: ESCHERICHIA COLI K12 (bacteria) / Variant (production host): DH10B / References: UniProt: Q5A9A4, leucine-tRNA ligase
#2: Chemical ChemComp-ANZ / [(6-AMINO-9H-PURIN-9-YL)-[5-FLUORO-1,3-DIHYDRO-1-HYDROXY-2,1-BENZOXABOROLE]-4'YL]METHYL DIHYDROGEN PHOSPHATE


Mass: 480.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H17BFN5O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.1 Å3/Da / Density % sol: 41.39 % / Description: NONE
Crystal growpH: 7.4
Details: 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: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 17, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2→50.57 Å / Num. obs: 16451 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.73
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.95 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WFG

2wfg


Resolution: 2→50.57 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.723 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23541 880 5.1 %RANDOM
Rwork0.17854 ---
obs0.18141 16451 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.337 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2→50.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1974 0 33 197 2204
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022120
X-RAY DIFFRACTIONr_bond_other_d0.0010.022011
X-RAY DIFFRACTIONr_angle_refined_deg1.49622892
X-RAY DIFFRACTIONr_angle_other_deg0.77834658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6575263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.93325.16193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68715369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.697158
X-RAY DIFFRACTIONr_chiral_restr0.1250.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212395
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02458
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_it1.0481.7521031
X-RAY DIFFRACTIONr_mcbond_other1.0461.7491030
X-RAY DIFFRACTIONr_mcangle_it1.7632.6161298
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4421.9891089
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→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 55 -
Rwork0.232 1163 -
obs--96.97 %

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