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- PDB-7c5c: Crystal structure of SeFRS -

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Basic information

Entry
Database: PDB / ID: 7c5c
TitleCrystal structure of SeFRS
ComponentsTyrosine--tRNA ligase
KeywordsLIGASE / AMINOACYL-TRNA SYNTHETASE
Function / homology
Function and homology information


tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / ATP binding / cytoplasm
Similarity search - Function
Tyrosine-tRNA ligase, type 3 / Tyrosine-tRNA ligase, archaeal/eukaryotic-type / Tyrosine-tRNA ligase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsSun, J.P. / Wang, J.Y. / Zhu, Z.L. / He, Q.T.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: To Be Published
Title: CRYSTAL STRUCTURE OF SeFRS
Authors: Sun, J.P. / Wang, J.Y. / Zhu, Z.L. / He, Q.T.
History
DepositionMay 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1473
Polymers36,0231
Non-polymers1242
Water3,657203
1
A: Tyrosine--tRNA ligase
hetero molecules

A: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2946
Polymers72,0452
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3680 Å2
ΔGint-16 kcal/mol
Surface area27890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.612, 38.776, 82.311
Angle α, β, γ (deg.)90.000, 91.143, 90.000
Int Tables number3
Space group name H-MP121
Space group name HallP2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
Components on special symmetry positions
IDModelComponents
11A-537-

HOH

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Components

#1: Protein Tyrosine--tRNA ligase / Aminoacyl-tRNA synthetase / Tyrosyl-tRNA synthetase / TyrRS


Mass: 36022.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Gene: tyrS, MJ0389 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57834, tyrosine-tRNA ligase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% Polyethylene glycol (PEG) 3350, 100mM Bis-Tris(pH5.5), 200mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.72→44.73 Å / Num. obs: 35051 / % possible obs: 97.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 31.21 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.032 / Rrim(I) all: 0.034 / Net I/σ(I): 25.9
Reflection shellResolution: 1.72→1.75 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1201 / CC1/2: 0.926 / Rrim(I) all: 0.387

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HJR

4hjr


Resolution: 1.72→44.73 Å / SU ML: 0.1883 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.9605 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2221 1766 5.04 %0.222
Rwork0.1881 33250 --
obs0.1899 35016 97.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.87 Å2
Refinement stepCycle: LAST / Resolution: 1.72→44.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2465 0 8 203 2676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00532556
X-RAY DIFFRACTIONf_angle_d0.76383443
X-RAY DIFFRACTIONf_chiral_restr0.0493383
X-RAY DIFFRACTIONf_plane_restr0.0044444
X-RAY DIFFRACTIONf_dihedral_angle_d18.08921601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.760.39781020.31681951X-RAY DIFFRACTION74.04
1.76-1.820.28911350.24962553X-RAY DIFFRACTION99.59
1.82-1.880.30311280.22882591X-RAY DIFFRACTION99.93
1.88-1.940.25171690.21852564X-RAY DIFFRACTION99.64
1.94-2.020.24151320.21532596X-RAY DIFFRACTION99.74
2.02-2.110.27011400.21872580X-RAY DIFFRACTION99.82
2.11-2.220.28821060.2052614X-RAY DIFFRACTION99.93
2.22-2.360.22511460.20692589X-RAY DIFFRACTION99.82
2.36-2.550.23291360.20342629X-RAY DIFFRACTION99.78
2.55-2.80.20711120.20652628X-RAY DIFFRACTION99.85
2.8-3.210.24751590.22621X-RAY DIFFRACTION100
3.21-4.040.2121530.17442623X-RAY DIFFRACTION99.86
4.04-44.730.18461480.15472711X-RAY DIFFRACTION99.24
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)
14.628381678461.063175185172.254505275521.669227727580.5200034126091.1268859250.398501075535-0.22271429867-0.3796214016030.120366657432-0.194247675136-0.1171173901330.161632840924-0.166776030016-0.1246250471340.221180082937-0.05831423667160.003390529748030.2556663556540.03137967189160.30003768258810.974875172-3.499280861318.0016368184
24.062384787290.4810948923823.399704506680.9229426433330.666461365582.98983420704-0.100634138251-0.1849796231390.1113233536150.00613917494346-0.0510117537551-0.0551719150922-0.212408732270.03331430281060.1291643985030.160801623104-0.01712633876810.03649792918120.241598768061-0.032906600280.2511578853836.321202812426.6378214465113.2233419117
34.401654694120.831923432730.2328180596734.230321337321.575459413473.76648787469-0.186157530442-0.08790726743510.02400913393290.2354412383020.157332666359-0.494873735447-0.07452964414990.220117541369-0.002150647570760.176623972138-0.012282380564-0.05727104395550.1879501090.03411291890160.27966632313533.65512693087.7725783485526.576376719
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 124 )
2X-RAY DIFFRACTION2chain 'A' and (resid 125 through 203 )
3X-RAY DIFFRACTION3chain 'A' and (resid 204 through 313 )

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