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- PDB-6jp2: Crystal structure of pyrrolysyl-tRNA synthetase from Methanomethy... -

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Basic information

Entry
Database: PDB / ID: 6jp2
TitleCrystal structure of pyrrolysyl-tRNA synthetase from Methanomethylophilus alvus
ComponentsPyrrolysyl-tRNA synthetasePyrrolysine—tRNAPyl ligase
KeywordsTRANSLATION / LIGASE / aminoacyl-tRNA synthetase / tRNA / pyrrolysyl-tRNA synthetase / non-natural amino acids
Function / homology
Function and homology information


pyrrolysine-tRNAPyl ligase / pyrrolysyl-tRNA synthetase activity
Similarity search - Function
Phenylalanyl tRNA synthetase beta chain, core domain / Phenylalanyl tRNA synthetase beta chain CLM domain / Pyrrolysyl-tRNA ligase, C-terminal / 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
Similarity search - Component
Biological speciesCandidatus Methanomethylophilus alvus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.272 Å
AuthorsYanagisawa, T. / Kuratani, M. / Yokoyama, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)24550203 Japan
Japan Agency for Medical Research and Development (AMED)JP17am0101081 Japan
CitationJournal: Acs Synth Biol / Year: 2020
Title: Fully Productive Cell-Free Genetic Code Expansion by Structure-Based Engineering ofMethanomethylophilus alvusPyrrolysyl-tRNA Synthetase.
Authors: Seki, E. / Yanagisawa, T. / Kuratani, M. / Sakamoto, K. / Yokoyama, S.
History
DepositionMar 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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: Pyrrolysyl-tRNA synthetase
B: Pyrrolysyl-tRNA synthetase
C: Pyrrolysyl-tRNA synthetase
D: Pyrrolysyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)124,5134
Polymers124,5134
Non-polymers00
Water5,783321
1
A: Pyrrolysyl-tRNA synthetase
C: Pyrrolysyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)62,2572
Polymers62,2572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-23 kcal/mol
Surface area24680 Å2
MethodPISA
2
B: Pyrrolysyl-tRNA synthetase
D: Pyrrolysyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)62,2572
Polymers62,2572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-24 kcal/mol
Surface area25060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.380, 112.780, 107.430
Angle α, β, γ (deg.)90.00, 114.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Pyrrolysyl-tRNA synthetase / Pyrrolysine—tRNAPyl ligase


Mass: 31128.367 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Methanomethylophilus alvus (archaea)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: M9SC49, pyrrolysine-tRNAPyl ligase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.5 Å3/Da / Density % sol: 50.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG3350, Cesium Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 23, 2017
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.27→49 Å / Num. obs: 55681 / % possible obs: 98.96 % / Redundancy: 3.7 % / Rrim(I) all: 0.089 / Net I/σ(I): 19.1
Reflection shellResolution: 2.27→2.31 Å / Redundancy: 3.5 % / Num. unique obs: 2345 / Rrim(I) all: 0.676

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZCE

2zce


Resolution: 2.272→48.991 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.21
RfactorNum. reflection% reflection
Rfree0.2567 2785 5 %
Rwork0.213 --
obs0.2152 55681 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.272→48.991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8619 0 0 321 8940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028778
X-RAY DIFFRACTIONf_angle_d0.51311835
X-RAY DIFFRACTIONf_dihedral_angle_d2.4425349
X-RAY DIFFRACTIONf_chiral_restr0.0391305
X-RAY DIFFRACTIONf_plane_restr0.0031538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.272-2.31120.33191240.28512345X-RAY DIFFRACTION89
2.3112-2.35320.29971390.2692638X-RAY DIFFRACTION99
2.3532-2.39850.31931390.26642658X-RAY DIFFRACTION99
2.3985-2.44750.321390.25542629X-RAY DIFFRACTION99
2.4475-2.50070.30921380.24212639X-RAY DIFFRACTION99
2.5007-2.55880.28391400.25372658X-RAY DIFFRACTION99
2.5588-2.62280.29011380.24642633X-RAY DIFFRACTION99
2.6228-2.69370.29631410.24172671X-RAY DIFFRACTION100
2.6937-2.7730.25591390.23522643X-RAY DIFFRACTION100
2.773-2.86250.29671390.24982649X-RAY DIFFRACTION100
2.8625-2.96480.29521410.24532681X-RAY DIFFRACTION100
2.9648-3.08350.28021400.23632650X-RAY DIFFRACTION100
3.0835-3.22380.24191400.22942664X-RAY DIFFRACTION100
3.2238-3.39370.28751390.23592641X-RAY DIFFRACTION100
3.3937-3.60630.2611420.21492692X-RAY DIFFRACTION100
3.6063-3.88460.24171390.18932650X-RAY DIFFRACTION100
3.8846-4.27530.23221410.18252679X-RAY DIFFRACTION100
4.2753-4.89350.20731420.16052693X-RAY DIFFRACTION100
4.8935-6.16340.2521420.19682688X-RAY DIFFRACTION100
6.1634-49.00210.22661430.20142695X-RAY DIFFRACTION98

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