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- PDB-3qo7: Crystal structure of the seryl-tRNA synthetase from Candida albicans -

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Basic information

Entry
Database: PDB / ID: 3qo7
TitleCrystal structure of the seryl-tRNA synthetase from Candida albicans
ComponentsSeryl-tRNA synthetase, cytoplasmic
KeywordsLIGASE / class-II aminoacyl-tRNA synthetase family / Type-1 seryl-tRNA synthetase subfamily / aminoacyl-tRNA synthetase / tRNA / serine / amino acid biosynthesis / CTG-clade / codon ambiguity / pathogen
Function / homology
Function and homology information


serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / cytoplasmic translation / tRNA binding / ATP binding / cytoplasm / cytosol
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
ADENOSINE-5'-TRIPHOSPHATE / Serine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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 9, 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 ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Seryl-tRNA synthetase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1902
Polymers55,6831
Non-polymers5071
Water1,04558
1
A: Seryl-tRNA synthetase, cytoplasmic
hetero molecules

A: Seryl-tRNA synthetase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,3804
Polymers111,3662
Non-polymers1,0142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area6040 Å2
ΔGint-18 kcal/mol
Surface area38390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.152, 91.152, 275.839
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-504-

HOH

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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: SES1, CaO19.7901 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HGT6, serine-tRNA ligase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.97 Å3/Da / Density % sol: 58.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion
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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.55→79.1 Å / Num. all: 23155 / Num. obs: 23155 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.6 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 8
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.57 / % possible all: 100

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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: 2.55→45.973 Å / SU ML: 0.27 / σ(F): 0 / Phase error: 21.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2157 1105 4.86 %
Rwork0.1776 --
obs0.1795 22755 98.64 %
all-22755 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.834 Å2 / ksol: 0.371 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.6087 Å20 Å2-0 Å2
2--7.6087 Å20 Å2
3----15.2174 Å2
Refinement stepCycle: LAST / Resolution: 2.55→45.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3552 0 31 58 3641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113688
X-RAY DIFFRACTIONf_angle_d1.3034983
X-RAY DIFFRACTIONf_dihedral_angle_d16.2061419
X-RAY DIFFRACTIONf_chiral_restr0.082527
X-RAY DIFFRACTIONf_plane_restr0.005648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5501-2.66610.31971160.24552549X-RAY DIFFRACTION95
2.6661-2.80670.25261300.22742588X-RAY DIFFRACTION97
2.8067-2.98250.26441270.20442662X-RAY DIFFRACTION99
2.9825-3.21270.25231570.18972651X-RAY DIFFRACTION99
3.2127-3.53590.2271430.17452695X-RAY DIFFRACTION99
3.5359-4.04730.21971260.15672740X-RAY DIFFRACTION100
4.0473-5.09810.18051470.13852797X-RAY DIFFRACTION100
5.0981-45.98060.1861590.19192968X-RAY DIFFRACTION100
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)
11.34170.55280.12770.2761-0.10920.6961-0.1081-0.0225-0.195-0.03830.0647-0.1664-0.12140.4945-0.07050.25510.0887-0.02540.4331-0.10560.339422.3574-31.81227.3733
21.2951-1.42080.85770.403-0.39490.55530.04390.31960.0963-0.0378-0.0335-0.07150.15850.1619-0.04080.38760.0167-0.02290.2756-0.03520.3135-20.5524-26.55360.897
30.9768-0.56210.15471.0706-0.03121.44750.14130.10810.0223-0.1139-0.0763-0.0845-0.04760.2524-0.0770.2155-0.01840.03660.221-0.04830.2391-17.6246-18.676919.6705
40.92650.07940.05250.0731-0.12341.03030.15490.1002-0.1005-0.1327-0.01490.00440.32010.0127-0.11320.29150.0489-0.0380.1596-0.06070.2163-22.4306-27.598610.4499
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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