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- PDB-8dqi: Crystal structure of pyrrolysyl-tRNA synthetase from Methanomethy... -

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Basic information

Entry
Database: PDB / ID: 8dqi
TitleCrystal structure of pyrrolysyl-tRNA synthetase from Methanomethylophilus alvus engineered for acridone amino acid (RS1) bound to ATP and acridone after 2- weeks of crystal growth
ComponentsAA_TRNA_LIGASE_II domain-containing protein
KeywordsLIGASE / Genetic code expansion / Methanomethylophilus alvus / pyrrolysyl-tRNA synthetase / acridone
Function / homology
Function and homology information


aminoacyl-tRNA ligase activity / ATP binding / 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 / 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
ADENOSINE-5'-TRIPHOSPHATE / Chem-T7Q / Aminoacyl-transfer RNA synthetases class-II family profile domain-containing protein
Similarity search - Component
Biological speciesCandidatus Methanomethylophilus alvus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsGottfried-Lee, I. / Karplus, P.A. / Mehl, R.A. / Cooley, R.B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM131168-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RM1-GM144227 United States
CitationJournal: Acs Chem.Biol. / Year: 2022
Title: Structures of Methanomethylophilus alvus Pyrrolysine tRNA-Synthetases Support the Need for De Novo Selections When Altering the Substrate Specificity.
Authors: Gottfried-Lee, I. / Perona, J.J. / Karplus, P.A. / Mehl, R.A. / Cooley, R.B.
History
DepositionJul 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: 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
D: AA_TRNA_LIGASE_II domain-containing protein
A: AA_TRNA_LIGASE_II domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,08712
Polymers61,3822
Non-polymers1,70610
Water8,467470
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-68 kcal/mol
Surface area22430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.795, 110.795, 113.774
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 DA

#1: Protein AA_TRNA_LIGASE_II domain-containing protein


Mass: 30690.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Methanomethylophilus alvus (archaea)
Gene: BKD89_05515 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3G3IHP7

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Non-polymers , 6 types, 480 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-T7Q / (2~{S})-2-azanyl-3-(9-oxidanylidene-10~{H}-acridin-2-yl)propanoic acid / acridone amino acid (RS1)


Type: peptide linking / Mass: 283.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 2.84 Å3/Da / Density % sol: 56.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: PEG 3350, Sodium citrate tribasic dihydrate, magnesium chloride
PH range: 5.0-6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.54→45.43 Å / Num. obs: 101122 / % possible obs: 100 % / Redundancy: 14.1 % / CC1/2: 1 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.023 / Rrim(I) all: 0.087 / Net I/σ(I): 16.9 / Num. measured all: 1428963 / Scaling rejects: 71
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
1.54-1.5714.22.797087649770.3570.7632.8931100
8.44-45.43130.026822663310.0080.02863.998.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6jp2

6jp2


Resolution: 1.54→45.43 Å / SU ML: 0.1883 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.668
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1858 5083 5.03 %
Rwork0.1665 96032 -
obs0.1675 101115 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.6 Å2
Refinement stepCycle: LAST / Resolution: 1.54→45.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4056 0 107 470 4633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00964320
X-RAY DIFFRACTIONf_angle_d1.08145862
X-RAY DIFFRACTIONf_chiral_restr0.0593652
X-RAY DIFFRACTIONf_plane_restr0.0099751
X-RAY DIFFRACTIONf_dihedral_angle_d14.11421605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.560.30681640.29333211X-RAY DIFFRACTION99.97
1.56-1.580.27271660.28413164X-RAY DIFFRACTION100
1.58-1.60.28091630.27413164X-RAY DIFFRACTION100
1.6-1.620.26831900.27733225X-RAY DIFFRACTION100
1.62-1.640.37571750.31943160X-RAY DIFFRACTION100
1.64-1.660.3691450.30263205X-RAY DIFFRACTION100
1.66-1.680.28771810.26963181X-RAY DIFFRACTION100
1.68-1.710.26131750.24853217X-RAY DIFFRACTION100
1.71-1.730.23521620.22653191X-RAY DIFFRACTION100
1.73-1.760.22921820.20853160X-RAY DIFFRACTION100
1.76-1.790.19571510.19313235X-RAY DIFFRACTION99.97
1.79-1.830.21131640.17923215X-RAY DIFFRACTION99.94
1.83-1.860.19321780.17863169X-RAY DIFFRACTION100
1.86-1.90.18761730.17443203X-RAY DIFFRACTION100
1.9-1.940.18161610.17843209X-RAY DIFFRACTION100
1.94-1.990.22251800.17763162X-RAY DIFFRACTION100
1.99-2.040.18671640.183194X-RAY DIFFRACTION100
2.04-2.090.20431690.15793218X-RAY DIFFRACTION100
2.09-2.150.16961710.15883198X-RAY DIFFRACTION100
2.15-2.220.1741770.15783173X-RAY DIFFRACTION100
2.22-2.30.1791620.14973221X-RAY DIFFRACTION100
2.3-2.390.19411680.15513184X-RAY DIFFRACTION99.97
2.39-2.50.16871680.15613214X-RAY DIFFRACTION100
2.5-2.630.19081660.16073221X-RAY DIFFRACTION100
2.63-2.80.18141730.16123180X-RAY DIFFRACTION100
2.8-3.010.18791740.16383233X-RAY DIFFRACTION100
3.01-3.320.17661770.15563189X-RAY DIFFRACTION100
3.32-3.80.14691720.14343217X-RAY DIFFRACTION100
3.8-4.780.14721640.13173254X-RAY DIFFRACTION100
4.79-45.430.19181680.1733265X-RAY DIFFRACTION99.68

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