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

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Basic information

Entry
Database: PDB / ID: 5agh
TitleCrystal structure of the LeuRS editing domain of Candida albicans Mutant K510A
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 / ACETATE ION / :
Function and homology information
Biological speciesCANDIDA ALBICANS (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 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_sheet / 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_sheet.number_strands / _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: POTENTIAL CYTOSOLIC LEUCYL TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5583
Polymers29,4391
Non-polymers1182
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.349, 41.104, 67.264
Angle α, β, γ (deg.)90.00, 106.71, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein POTENTIAL CYTOSOLIC LEUCYL TRNA SYNTHETASE


Mass: 29439.432 Da / Num. of mol.: 1 / Fragment: EDITING DOMAIN (CP1), UNP RESIDUES 280-530 / Mutation: YES
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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.01 Å3/Da / Density % sol: 38.75 % / Description: NONE
Crystal growpH: 4
Details: 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM ACETATE TRIHYDRATE PH 4.0, 24% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.81→64 Å / Num. obs: 18976 / % possible obs: 90.5 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.8
Reflection shellResolution: 1.81→1.85 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.6 / % possible all: 49

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Processing

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

2wfg


Resolution: 1.81→64.42 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.045 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.21844 998 5.1 %RANDOM
Rwork0.1651 ---
obs0.16776 18676 90.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.545 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20.5 Å2
2---0.52 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.81→64.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1932 0 8 147 2087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021993
X-RAY DIFFRACTIONr_bond_other_d0.0010.021906
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.9822701
X-RAY DIFFRACTIONr_angle_other_deg0.75734412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9945249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.78925.28189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.64915350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.777157
X-RAY DIFFRACTIONr_chiral_restr0.0860.2301
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212246
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02423
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_it1.9812.443986
X-RAY DIFFRACTIONr_mcbond_other1.9792.438983
X-RAY DIFFRACTIONr_mcangle_it3.2263.6381228
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6192.8871006
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: 1.806→1.852 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 34 -
Rwork0.213 747 -
obs--48.75 %
Refinement TLS params.Method: refined / Origin x: 38.186 Å / Origin y: -8.692 Å / Origin z: -48.172 Å
111213212223313233
T0.0936 Å2-0.0666 Å20.0234 Å2-0.1454 Å2-0.1046 Å2--0.244 Å2
L0.0886 °2-0.1693 °2-0.6552 °2-1.6452 °20.169 °2--5.962 °2
S0.0065 Å °-0.0779 Å °0.0933 Å °-0.3173 Å °0.3875 Å °-0.373 Å °0.2067 Å °0.3655 Å °-0.394 Å °

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