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- PDB-8ris: Computationally redesigend variant of Pyrrolysyl-tRNA Synthetase ... -

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Basic information

Entry
Database: PDB / ID: 8ris
TitleComputationally redesigend variant of Pyrrolysyl-tRNA Synthetase (Y306A)
ComponentsPyrrolysine--tRNA ligase
KeywordsLIGASE / Pyrrolysyl-tRNA synthetase
Function / homology
Function and homology information


pyrrolysine-tRNAPyl ligase / pyrrolysyl-tRNA synthetase activity / tRNA aminoacylation for protein translation / tRNA binding / ATP binding / cytoplasm
Similarity search - Function
Pyrrolysyl-tRNA ligase / Pyrrolysyl-tRNA ligase, N-terminal / Pyrrolysyl-tRNA ligase, C-terminal / Phenylalanyl-tRNA synthetase / tRNA synthetases class II core domain (F) / 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
Pyrrolysine--tRNA ligase
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsOberdorfer, G. / Moser, M. / Stoll, D.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)802217European Union
CitationJournal: To Be Published
Title: Computationally redesigend variant of Pyrrolysyl-tRNA Synthetase (Y306A)
Authors: Oberdorfer, G. / Moser, M. / Stoll, D.
History
DepositionDec 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyrrolysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7068
Polymers31,0751
Non-polymers6327
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.306, 104.306, 70.807
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Space group name HallP64
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Pyrrolysine--tRNA ligase / Pyrrolysine--tRNA(Pyl) ligase / Pyrrolysyl-tRNA synthetase / PylRS


Mass: 31074.615 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea) / Gene: pylS, MM_1445 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PWY1, pyrrolysine-tRNAPyl ligase

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Non-polymers , 5 types, 72 molecules

#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 3.58 Å3/Da / Density % sol: 65.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 0.05M L-Arginine, 0.05M L-Glutamic acid monosodium salt hydrate, 28% v/v PEG Smear Broad, 5% v/v Glycerol, drop ratio 1:1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873128 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 2.7→45.17 Å / Num. obs: 12180 / % possible obs: 99.92 % / Redundancy: 19.3 % / Biso Wilson estimate: 71.64 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.2166 / Rpim(I) all: 0.05042 / Rrim(I) all: 0.2225 / Net I/σ(I): 12.17
Reflection shellResolution: 2.7→2.797 Å / Redundancy: 18.2 % / Rmerge(I) obs: 3.112 / Mean I/σ(I) obs: 0.97 / Num. unique obs: 1207 / CC1/2: 0.514 / CC star: 0.824 / Rpim(I) all: 0.7564 / Rrim(I) all: 3.239 / % possible all: 99.92

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
autoPROCdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→45.17 Å / SU ML: 0.4613 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.9922
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2438 609 5 %
Rwork0.2166 11564 -
obs0.218 12173 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.82 Å2
Refinement stepCycle: LAST / Resolution: 2.7→45.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 41 65 2148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00122175
X-RAY DIFFRACTIONf_angle_d0.40242931
X-RAY DIFFRACTIONf_chiral_restr0.0388321
X-RAY DIFFRACTIONf_plane_restr0.0041384
X-RAY DIFFRACTIONf_dihedral_angle_d8.1762833
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.970.37751510.33162874X-RAY DIFFRACTION99.9
2.97-3.40.27291510.262866X-RAY DIFFRACTION99.93
3.4-4.280.22071510.2022879X-RAY DIFFRACTION100
4.29-45.170.22461560.19432945X-RAY DIFFRACTION99.94

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