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- PDB-7r6o: Pyrrolysyl-tRNA synthetase from methanogenic archaeon ISO4-G1 (G1... -

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Basic information

Entry
Database: PDB / ID: 7r6o
TitlePyrrolysyl-tRNA synthetase from methanogenic archaeon ISO4-G1 (G1PylRS)
ComponentsPyrrolysyl-tRNA synthetase PylS
KeywordsTRANSLATION / tRNA synthetases / tRNA-ligase / tRNA synthetases class II
Function / homology
Function and homology information


aminoacyl-tRNA ligase activity / tRNA aminoacylation / tRNA binding / ATP binding
Similarity search - Function
Pyrrolysyl-tRNA ligase, C-terminal / Phenylalanyl-tRNA synthetase / tRNA synthetases class II core domain (F) / 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) / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Pyrrolysyl-tRNA synthetase PylS
Similarity search - Component
Biological speciesmethanogenic archaeon mixed culture ISO4-G1 (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFrkic, R.L. / Huber, T. / Jackson, C.J.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP200100348 Australia
Australian Research Council (ARC)DP21010088 Australia
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Genetic Encoding of Cyanopyridylalanine for In-Cell Protein Macrocyclization by the Nitrile-Aminothiol Click Reaction.
Authors: Abdelkader, E.H. / Qianzhu, H. / George, J. / Frkic, R.L. / Jackson, C.J. / Nitsche, C. / Otting, G. / Huber, T.
History
DepositionJun 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyrrolysyl-tRNA synthetase PylS
B: Pyrrolysyl-tRNA synthetase PylS
C: Pyrrolysyl-tRNA synthetase PylS
D: Pyrrolysyl-tRNA synthetase PylS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,8558
Polymers123,5724
Non-polymers2824
Water11,241624
1
A: Pyrrolysyl-tRNA synthetase PylS
C: Pyrrolysyl-tRNA synthetase PylS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9104
Polymers61,7862
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-21 kcal/mol
Surface area24840 Å2
MethodPISA
2
B: Pyrrolysyl-tRNA synthetase PylS
hetero molecules

D: Pyrrolysyl-tRNA synthetase PylS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9444
Polymers61,7862
Non-polymers1582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_546-x,y-1/2,-z+11
Buried area4590 Å2
ΔGint-36 kcal/mol
Surface area24750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.855, 81.348, 121.845
Angle α, β, γ (deg.)90.000, 102.142, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein
Pyrrolysyl-tRNA synthetase PylS


Mass: 30893.084 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) methanogenic archaeon mixed culture ISO4-G1 (environmental samples)
Gene: AUP07_0651 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A126QV54
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 624 / 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: 2.31 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 30% w/v PEG 4000, 100mM Tris-HCl (pH 9.0), 200mM lithium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→48.01 Å / Num. obs: 57200 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 44.25 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.063 / Rrim(I) all: 0.168 / Net I/σ(I): 6.7 / Num. measured all: 401958 / Scaling rejects: 26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.267.12.3083190844730.3410.9292.490.999.9
9.59-48.016.80.04349737360.9990.0170.0462199

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JP2

6jp2


Resolution: 2.2→46.56 Å / SU ML: 0.3628 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.3116
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2686 2916 5.1 %
Rwork0.219 54220 -
obs0.2214 57136 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.06 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8660 0 17 624 9301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00198849
X-RAY DIFFRACTIONf_angle_d0.464111908
X-RAY DIFFRACTIONf_chiral_restr0.03721288
X-RAY DIFFRACTIONf_plane_restr0.00351544
X-RAY DIFFRACTIONf_dihedral_angle_d11.18183339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.30871340.30582563X-RAY DIFFRACTION99.89
2.24-2.270.39021290.31832603X-RAY DIFFRACTION99.74
2.27-2.320.35661330.3092550X-RAY DIFFRACTION99.93
2.32-2.360.34661550.30682538X-RAY DIFFRACTION99.89
2.36-2.410.33671160.30552591X-RAY DIFFRACTION99.89
2.41-2.460.3741350.30042608X-RAY DIFFRACTION99.96
2.46-2.520.38491640.29472540X-RAY DIFFRACTION99.93
2.52-2.580.32231330.28832562X-RAY DIFFRACTION99.89
2.58-2.650.31591540.26912576X-RAY DIFFRACTION99.93
2.65-2.730.29641550.2612523X-RAY DIFFRACTION99.89
2.73-2.820.32211470.26032586X-RAY DIFFRACTION99.96
2.82-2.920.32721490.26542570X-RAY DIFFRACTION100
2.92-3.030.3021400.25092587X-RAY DIFFRACTION99.93
3.03-3.170.31771540.24792548X-RAY DIFFRACTION99.96
3.17-3.340.32791380.23552596X-RAY DIFFRACTION99.85
3.34-3.550.2731440.21732569X-RAY DIFFRACTION99.93
3.55-3.820.26371260.19252591X-RAY DIFFRACTION99.82
3.82-4.210.20051240.17762640X-RAY DIFFRACTION99.82
4.21-4.820.19461170.16492604X-RAY DIFFRACTION99.89
4.82-6.060.2081310.18392623X-RAY DIFFRACTION99.89
6.07-46.560.21151380.17422652X-RAY DIFFRACTION98.9

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