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- PDB-7u0r: Crystal structure of Methanomethylophilus alvus PylRS(N166A/V168A... -

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Basic information

Entry
Database: PDB / ID: 7u0r
TitleCrystal structure of Methanomethylophilus alvus PylRS(N166A/V168A) complexed with meta-trifluoromethyl-2-benzylmalonate and AMP-PNP
ComponentsPyrrolysyl-tRNA synthetase
KeywordsTRANSLATION/INHIBITOR / aminoacyl-tRNA synthetase / ligase / non-natural amino acids / pyrrolysyl-tRNA synthetase / TRANSLATION / TRANSLATION-INHIBITOR complex
Function / homology
Function and homology information


pyrrolysine-tRNAPyl ligase / pyrrolysyl-tRNA synthetase activity / metal ion binding
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-LE0 / Pyrrolysyl-tRNA synthetase
Similarity search - Component
Biological speciesCandidatus Methanomethylophilus alvus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSwenson, C.V. / Roe, L.T. / Fricke, R.C.B. / Smaga, S.S. / Gee, C.L. / Schepartz, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-2002182 United States
CitationJournal: Nat.Chem. / Year: 2023
Title: Expanding the substrate scope of pyrrolysyl-transfer RNA synthetase enzymes to include non-alpha-amino acids in vitro and in vivo.
Authors: Fricke, R. / Swenson, C.V. / Roe, L.T. / Hamlish, N.X. / Shah, B. / Zhang, Z. / Ficaretta, E. / Ad, O. / Smaga, S. / Gee, C.L. / Chatterjee, A. / Schepartz, A.
History
DepositionFeb 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 25, 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
B: Pyrrolysyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,89512
Polymers62,1152
Non-polymers1,78010
Water8,161453
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-64 kcal/mol
Surface area23600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.958, 108.958, 112.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Pyrrolysyl-tRNA synthetase


Mass: 31057.293 Da / Num. of mol.: 2 / Mutation: N166A, V168A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Methanomethylophilus alvus (archaea)
Gene: MMALV_11280 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: M9SC49, pyrrolysine-tRNAPyl ligase

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Non-polymers , 5 types, 463 molecules

#2: Chemical ChemComp-LE0 / {[3-(trifluoromethyl)phenyl]methyl}propanedioic acid


Mass: 262.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H9F3O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.68 Å3/Da / Density % sol: 54.14 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 10 mM Tris-HCl pH 7.4, 26% polyethylene glycol 3350, 100 mM meta-trifluoromethyl-2-benzylmalonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 1.8→45.37 Å / Num. obs: 57972 / % possible obs: 95.02 % / Redundancy: 1.997 % / Biso Wilson estimate: 39.02 Å2 / CC1/2: 1 / CC star: 1 / Net I/σ(I): 18.75
Reflection shellResolution: 1.803→1.867 Å / Num. unique obs: 4659 / CC1/2: 0.106 / % possible all: 66.69

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6jp2

6jp2


Resolution: 1.8→45.37 Å / SU ML: 0.3113 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.4297
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2114 2924 5.11 %
Rwork0.18 54351 -
obs0.1817 57275 95.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.8 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4332 0 111 453 4896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01144562
X-RAY DIFFRACTIONf_angle_d1.10436179
X-RAY DIFFRACTIONf_chiral_restr0.0655671
X-RAY DIFFRACTIONf_plane_restr0.0091796
X-RAY DIFFRACTIONf_dihedral_angle_d15.49591713
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.4328920.43511510X-RAY DIFFRACTION55.92
1.83-1.860.44361120.3982037X-RAY DIFFRACTION75.59
1.86-1.90.40561070.35842294X-RAY DIFFRACTION84.69
1.9-1.930.36141200.32892453X-RAY DIFFRACTION89.5
1.93-1.970.35141400.29892518X-RAY DIFFRACTION93.1
1.97-2.020.27531050.26522673X-RAY DIFFRACTION96.79
2.02-2.060.32161590.23282703X-RAY DIFFRACTION99.83
2.06-2.120.27691500.2292704X-RAY DIFFRACTION99.96
2.12-2.170.26881250.21152727X-RAY DIFFRACTION100
2.17-2.240.23761250.21542761X-RAY DIFFRACTION100
2.24-2.310.281440.21072688X-RAY DIFFRACTION100
2.31-2.390.28291630.19542729X-RAY DIFFRACTION100
2.39-2.490.21521660.19522707X-RAY DIFFRACTION100
2.49-2.60.23591620.18312698X-RAY DIFFRACTION100
2.6-2.740.28211130.20082781X-RAY DIFFRACTION100
2.74-2.910.2171360.18662698X-RAY DIFFRACTION100
2.91-3.130.22731320.1932757X-RAY DIFFRACTION100
3.13-3.450.21491660.17722700X-RAY DIFFRACTION100
3.45-3.950.17791940.15062705X-RAY DIFFRACTION100
3.95-4.970.13291630.13312733X-RAY DIFFRACTION100
4.97-45.370.20671500.15992775X-RAY DIFFRACTION99.83

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