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- PDB-5ud5: Crystal structure of the tRNA binding domain of Pyrrolysyl-tRNA s... -

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Basic information

Entry
Database: PDB / ID: 5ud5
TitleCrystal structure of the tRNA binding domain of Pyrrolysyl-tRNA synthetase bound to tRNA(Pyl)
Components
  • Pyrrolysine--tRNA ligase
  • RNA (70-MER)
KeywordsLIGASE/RNA / PylRS / tRNA / aminoacyl-tRNA synthetase / LIGASE-RNA complex
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
: / RNA / RNA (> 10) / Pyrrolysine--tRNA ligase
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
Methanosarcina mazei Go1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.347 Å
AuthorsSuzuki, T. / Soll, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM22854 United States
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Crystal structures reveal an elusive functional domain of pyrrolysyl-tRNA synthetase.
Authors: Suzuki, T. / Miller, C. / Guo, L.T. / Ho, J.M.L. / Bryson, D.I. / Wang, Y.S. / Liu, D.R. / Soll, D.
History
DepositionDec 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 1, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyrrolysine--tRNA ligase
B: Pyrrolysine--tRNA ligase
C: RNA (70-MER)
D: RNA (70-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5696
Polymers71,4394
Non-polymers1312
Water43224
1
A: Pyrrolysine--tRNA ligase
C: RNA (70-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7853
Polymers35,7192
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-21 kcal/mol
Surface area15680 Å2
MethodPISA
2
B: Pyrrolysine--tRNA ligase
D: RNA (70-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7853
Polymers35,7192
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-20 kcal/mol
Surface area15840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.280, 72.280, 238.970
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 12604.611 Da / Num. of mol.: 2 / Fragment: UNP residues 1-101
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88) (archaea)
Strain: ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88
Gene: pylS, MM_1445 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PWY1, pyrrolysine-tRNAPyl ligase
#2: RNA chain RNA (70-MER)


Mass: 23114.709 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Methanosarcina mazei Go1 (archaea) / References: GenBank: 20986624
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: HEPES, magnesium chloride, PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.347→49.22 Å / Num. obs: 31207 / % possible obs: 99.7 % / Redundancy: 9.79 % / Net I/σ(I): 22.57

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.347→49.218 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.75
RfactorNum. reflection% reflection
Rfree0.2423 3124 10.01 %
Rwork0.2164 --
obs0.2191 31207 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.347→49.218 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1394 3020 0 24 4438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044787
X-RAY DIFFRACTIONf_angle_d0.8357139
X-RAY DIFFRACTIONf_dihedral_angle_d12.2992580
X-RAY DIFFRACTIONf_chiral_restr0.04922
X-RAY DIFFRACTIONf_plane_restr0.005374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3465-2.38320.36391310.34251184X-RAY DIFFRACTION95
2.3832-2.42230.34421430.33751276X-RAY DIFFRACTION100
2.4223-2.4640.36641350.31551227X-RAY DIFFRACTION100
2.464-2.50880.35391430.33061273X-RAY DIFFRACTION100
2.5088-2.55710.39431400.34241243X-RAY DIFFRACTION100
2.5571-2.60930.36411360.32781260X-RAY DIFFRACTION100
2.6093-2.6660.33231440.31961273X-RAY DIFFRACTION100
2.666-2.7280.33741400.31061244X-RAY DIFFRACTION100
2.728-2.79620.35531350.32361268X-RAY DIFFRACTION100
2.7962-2.87180.33751410.30851268X-RAY DIFFRACTION100
2.8718-2.95630.30211400.27791246X-RAY DIFFRACTION100
2.9563-3.05170.281450.26241277X-RAY DIFFRACTION100
3.0517-3.16080.3031420.25021270X-RAY DIFFRACTION100
3.1608-3.28730.25451410.21821296X-RAY DIFFRACTION100
3.2873-3.43690.21081410.21071260X-RAY DIFFRACTION100
3.4369-3.6180.22431450.22471271X-RAY DIFFRACTION100
3.618-3.84460.22211400.18721283X-RAY DIFFRACTION100
3.8446-4.14140.22141480.18791292X-RAY DIFFRACTION100
4.1414-4.55780.20631390.17831308X-RAY DIFFRACTION100
4.5578-5.21670.20991500.17331315X-RAY DIFFRACTION100
5.2167-6.57010.24951460.19091341X-RAY DIFFRACTION100
6.5701-49.22880.19681590.19551408X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -4.2876 Å / Origin y: 40.8209 Å / Origin z: 97.9638 Å
111213212223313233
T0.6193 Å2-0.1135 Å20.0793 Å2-0.5296 Å2-0.0913 Å2--0.3927 Å2
L1.3561 °20.3153 °20.0443 °2-2.1008 °2-0.4579 °2--1.0128 °2
S-0.145 Å °0.1455 Å °-0.1067 Å °-0.3061 Å °0.1486 Å °-0.1091 Å °-0.0133 Å °-0.0126 Å °-0.0063 Å °
Refinement TLS groupSelection details: all

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