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- PDB-8p1z: Arabidopsis thaliana cytosolic seryl-tRNA synthetase in addition ... -

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Basic information

Entry
Database: PDB / ID: 8p1z
TitleArabidopsis thaliana cytosolic seryl-tRNA synthetase in addition of dithiothreitol (DTT)
ComponentsSerine--tRNA ligase, cytoplasmic
KeywordsCYTOSOLIC PROTEIN / synthetase / class II / cytoplasmic
Function / homology
Function and homology information


seryl-tRNA aminoacylation / serine-tRNA ligase / serine-tRNA ligase activity / plastid / cytoplasmic translation / ATP binding / cytosol
Similarity search - Function
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) / 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)
Similarity search - Domain/homology
Serine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKekez, I. / Soic, R. / Rokov-Plavec, J. / Matkovic-Calogovic, D.
Funding support Croatia, 1items
OrganizationGrant numberCountry
Croatian Science FoundationIP-2014-09-4274 Croatia
CitationJournal: To Be Published
Title: Arabidopsis thaliana cytosolic seryl-tRNA synthetase in addition of dithiothreitol (DTT)
Authors: Kekez, I. / Soic, R. / Rokov-Plavec, J. / Matkovic-Calogovic, D.
History
DepositionMay 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Serine--tRNA ligase, cytoplasmic


Theoretical massNumber of molelcules
Total (without water)52,1431
Polymers52,1431
Non-polymers00
Water86548
1
AAA: Serine--tRNA ligase, cytoplasmic

AAA: Serine--tRNA ligase, cytoplasmic


  • defined by author
  • Evidence: gel filtration
  • 104 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)104,2872
Polymers104,2872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area4820 Å2
ΔGint-26 kcal/mol
Surface area35700 Å2
Unit cell
Length a, b, c (Å)97.410, 45.889, 107.068
Angle α, β, γ (deg.)90.000, 93.942, 90.000
Int Tables number5
Space group name H-MI121

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Components

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


Mass: 52143.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Parts of the sequence that are not visible from the electron density map and are missing in pdb file.
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g27470, F21A20_180 / Production host: Escherichia coli (E. coli) / References: UniProt: Q39230, serine-tRNA ligase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.29 Å3/Da / Density % sol: 46.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: Magnesium chloride, PEG 4000, TRIS pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→19.167 Å / Num. obs: 20826 / % possible obs: 97.8 % / Redundancy: 6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.6
Reflection shellResolution: 2.3→2.39 Å / Rmerge(I) obs: 0.816 / Num. unique obs: 2088

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
CrysalisProdata reduction
CrysalisProdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.158 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.898 / WRfactor Rfree: 0.274 / WRfactor Rwork: 0.207 / SU B: 16.306 / SU ML: 0.341 / Average fsc free: 0.7249 / Average fsc work: 0.7458 / Cross valid method: FREE R-VALUE / ESU R: 0.382 / ESU R Free: 0.279
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2888 1080 5.187 %
Rwork0.2263 19741 -
all0.229 --
obs-20821 97.728 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 50.999 Å2
Baniso -1Baniso -2Baniso -3
1--0.001 Å20 Å20.006 Å2
2--0.001 Å20 Å2
3----0.001 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3256 0 0 48 3304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133331
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173093
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.6464490
X-RAY DIFFRACTIONr_angle_other_deg1.2461.5787169
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.0135.218413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.96522.5184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.82915600
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg6.524153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0151523
X-RAY DIFFRACTIONr_chiral_restr0.0620.2430
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023962
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02711
X-RAY DIFFRACTIONr_nbd_refined0.1970.2699
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.22955
X-RAY DIFFRACTIONr_nbtor_refined0.1620.21575
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21613
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1540.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2280.29
X-RAY DIFFRACTIONr_nbd_other0.2170.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1510.22
X-RAY DIFFRACTIONr_mcbond_it3.9375.3881634
X-RAY DIFFRACTIONr_mcbond_other3.9375.3871633
X-RAY DIFFRACTIONr_mcangle_it6.338.0512036
X-RAY DIFFRACTIONr_mcangle_other6.3298.0522037
X-RAY DIFFRACTIONr_scbond_it3.8475.6741697
X-RAY DIFFRACTIONr_scbond_other3.8465.6741698
X-RAY DIFFRACTIONr_scangle_it6.3458.3412453
X-RAY DIFFRACTIONr_scangle_other6.3448.3412454
X-RAY DIFFRACTIONr_lrange_it10.91999.56713581
X-RAY DIFFRACTIONr_lrange_other10.91999.57213573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.394690.3941331X-RAY DIFFRACTION91.683
2.36-2.4240.412730.3791415X-RAY DIFFRACTION97.1279
2.424-2.4950.369650.3721388X-RAY DIFFRACTION98.7092
2.495-2.5710.357790.3621365X-RAY DIFFRACTION99.244
2.571-2.6550.376830.3681274X-RAY DIFFRACTION99.0511
2.655-2.7490.444820.321262X-RAY DIFFRACTION99.1882
2.749-2.8520.332580.2951237X-RAY DIFFRACTION99.0819
2.852-2.9680.331740.2571182X-RAY DIFFRACTION99.2101
2.968-3.10.3550.2451120X-RAY DIFFRACTION99.2399
3.1-3.2510.278560.2131116X-RAY DIFFRACTION99.0702
3.251-3.4270.29580.21023X-RAY DIFFRACTION99.3566
3.427-3.6340.227410.201998X-RAY DIFFRACTION99.4258
3.634-3.8840.28470.176940X-RAY DIFFRACTION99.2958
3.884-4.1950.206470.169843X-RAY DIFFRACTION98.6696
4.195-4.5930.236500.151800X-RAY DIFFRACTION99.1832
4.593-5.1330.172370.145728X-RAY DIFFRACTION98.4556
5.133-5.9230.316400.178614X-RAY DIFFRACTION97.7578
5.923-7.2420.289340.197532X-RAY DIFFRACTION96.2585
7.242-10.1940.256240.19401X-RAY DIFFRACTION92.7948
10.194-19.1580.34380.225173X-RAY DIFFRACTION65.5797

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