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- PDB-3qne: Candida albicans seryl-tRNA synthetase -

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Basic information

Entry
Database: PDB / ID: 3qne
TitleCandida albicans seryl-tRNA synthetase
ComponentsSeryl-tRNA synthetase, cytoplasmic
KeywordsLIGASE / amino acid biosynthesis / CTG-clade / codon ambiguity / pathogen / class-II aminoacyl-tRNA synthetase family / Type-1 seryl-tRNA synthetase subfamily / tRNA / serine
Function / homology
Function and homology information


serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / cytoplasmic translation / ATP binding / cytosol / cytoplasm
Similarity search - Function
Serine-tRNA synthetase, tRNA binding domain / Serine-tRNA synthetase, type1, N-terminal / Seryl-tRNA synthetase N-terminal domain / Serine-tRNA ligase, type1 / Serine-tRNA ligase catalytic core domain / Serine-tRNA synthetase, type1, N-terminal domain superfamily / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Bira Bifunctional Protein; Domain 2 ...Serine-tRNA synthetase, tRNA binding domain / Serine-tRNA synthetase, type1, N-terminal / Seryl-tRNA synthetase N-terminal domain / Serine-tRNA ligase, type1 / Serine-tRNA ligase catalytic core domain / Serine-tRNA synthetase, type1, N-terminal domain superfamily / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Serine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRocha, R. / Santos, M.A. / Pereira, P.J.B. / Macedo-Ribeiro, S.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Unveiling the structural basis for translational ambiguity tolerance in a human fungal pathogen.
Authors: Rocha, R. / Pereira, P.J. / Santos, M.A. / Macedo-Ribeiro, S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Purification, crystallization and preliminary X-ray diffraction analysis of the seryl-tRNA synthetase from Candida albicans.
Authors: Rocha, R. / Barbosa Pereira, P.J. / Santos, M.A. / Macedo-Ribeiro, S.
History
DepositionFeb 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2011Group: Database references
Revision 1.2Aug 31, 2011Group: Database references
Revision 1.3Sep 14, 2011Group: Database references
Revision 1.4Sep 10, 2014Group: Database references
Revision 1.5Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Seryl-tRNA synthetase, cytoplasmic


Theoretical massNumber of molelcules
Total (without water)55,6831
Polymers55,6831
Non-polymers00
Water5,873326
1
A: Seryl-tRNA synthetase, cytoplasmic

A: Seryl-tRNA synthetase, cytoplasmic


Theoretical massNumber of molelcules
Total (without water)111,3662
Polymers111,3662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area4570 Å2
ΔGint-24 kcal/mol
Surface area38640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.050, 90.050, 276.757
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Seryl-tRNA synthetase, cytoplasmic / Serine--tRNA ligase / SerRS / Seryl-tRNA(Ser/Sec) synthetase


Mass: 55682.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Gene: CaO19.7901, SES1 / Plasmid: p7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q9HGT6, serine-tRNA ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.91 Å3/Da / Density % sol: 57.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.6
Details: 3.2-3.4 M ammonium sulfate, 0-2% v/v glycerol, 100 mM MES/sodium, pH 5.6-5.8, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 7, 2008
RadiationMonochromator: sagitally focusing Ge (220) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→78.1 Å / Num. obs: 43773 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.8 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 7.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 15 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 3.1 / % possible all: 78

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DQ0

2dq0


Resolution: 2→67.939 Å / SU ML: 0.23 / σ(F): 0 / σ(I): 0 / Phase error: 18.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2065 2197 5.06 %random
Rwork0.1652 ---
obs0.1673 43422 94.54 %-
all-43422 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.022 Å2 / ksol: 0.382 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.3115 Å2-0 Å2-0 Å2
2--4.3115 Å20 Å2
3----8.623 Å2
Refinement stepCycle: LAST / Resolution: 2→67.939 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3555 0 0 326 3881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013653
X-RAY DIFFRACTIONf_angle_d1.1574932
X-RAY DIFFRACTIONf_dihedral_angle_d14.1331403
X-RAY DIFFRACTIONf_chiral_restr0.087526
X-RAY DIFFRACTIONf_plane_restr0.005646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9997-2.07120.23421560.17373036X-RAY DIFFRACTION72
2.0712-2.15410.22082210.16073874X-RAY DIFFRACTION91
2.1541-2.25210.21212530.1654061X-RAY DIFFRACTION96
2.2521-2.37090.25592090.16984161X-RAY DIFFRACTION96
2.3709-2.51940.21012290.16014156X-RAY DIFFRACTION97
2.5194-2.7140.21172100.17124235X-RAY DIFFRACTION98
2.714-2.98710.22242070.18044289X-RAY DIFFRACTION98
2.9871-3.41930.21262490.17164298X-RAY DIFFRACTION99
3.4193-4.30790.20652120.14624431X-RAY DIFFRACTION99
4.3079-67.97850.17612510.16984684X-RAY DIFFRACTION99
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)
11.7639-0.9793-1.134-0.03080.18080.64050.00850.13840.03480.023-0.0309-0.08680.09580.123-0.03420.2026-0.07170.06470.3253-0.11870.250622.217331.2727-27.5898
20.62590.3451-0.28330.1307-0.11180.44030.0334-0.1394-0.0401-0.00360.0160.0022-0.11680.0213-0.04770.1801-0.00570.04140.1569-0.01090.1505-20.343726.1078-0.9951
30.81820.6364-0.39910.5192-0.26620.92440.098-0.0475-0.05480.0513-0.0563-0.067-0.03270.1214-0.04610.10870.01110.00190.1072-0.00670.1227-17.728518.5861-19.7176
40.5216-0.2161-0.04730.08720.0281.18010.0898-0.08230.04030.02610.01490.0432-0.199-0.0062-0.10020.1313-0.00610.03630.0876-0.01830.1173-22.558327.2023-10.2827
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:101)
2X-RAY DIFFRACTION2(chain A and resid 102:162)
3X-RAY DIFFRACTION3(chain A and resid 163:297)
4X-RAY DIFFRACTION4(chain A and resid 298:452)

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