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

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Basic information

Entry
Database: PDB / ID: 8dqj
TitleCrystal structure of pyrrolysyl-tRNA synthetase from Methanomethylophilus alvus engineered for acridone amino acid (AST) bound to ATP and acridone
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 MONOPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / DI(HYDROXYETHYL)ETHER / 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)62,91110
Polymers61,5022
Non-polymers1,4098
Water6,738374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6920 Å2
ΔGint-51 kcal/mol
Surface area22040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.722, 110.722, 114.157
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
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: 30750.914 Da / Num. of mol.: 2 / Mutation: N166S V168C W239T
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 , 7 types, 382 molecules

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


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: 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
#6: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 56.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Sodium citrate tribasic dihydrate

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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→35.12 Å / Num. obs: 101330 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 25.97 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.029 / Rrim(I) all: 0.103 / Net I/σ(I): 10.6 / Num. measured all: 1312985 / Scaling rejects: 187
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
1.54-1.57132.5016473549930.3480.7172.6041.1100
8.43-35.1211.80.04674446320.9970.0140.04929.597.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JP2

6jp2


Resolution: 1.54→35.12 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.193 5094 5.03 %
Rwork0.1703 96129 -
obs0.1715 101223 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.76 Å2 / Biso mean: 39.8651 Å2 / Biso min: 17.69 Å2
Refinement stepCycle: final / Resolution: 1.54→35.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3967 0 139 374 4480
Biso mean--45.49 37.82 -
Num. residues----522
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.54-1.560.37471730.3632053378
1.56-1.580.35481870.335631193306
1.58-1.60.29021610.302632083369
1.6-1.620.3341710.271931983369
1.62-1.640.27871580.257131813339
1.64-1.660.26131790.24131773356
1.66-1.680.271770.244331883365
1.68-1.710.23991710.2331943365
1.71-1.730.2381590.225832173376
1.73-1.760.2671770.232131913368
1.76-1.790.24411730.231631913364
1.79-1.830.27121710.214232043375
1.83-1.860.23951710.201431883359
1.86-1.90.21481590.186532183377
1.9-1.940.1921700.179432133383
1.94-1.990.19811620.166731833345
1.99-2.030.18251680.160331863354
2.04-2.090.20031810.168932213402
2.09-2.150.18911630.171732133376
2.15-2.220.21341700.168931933363
2.22-2.30.17771690.154832123381
2.3-2.390.16041640.156932083372
2.39-2.50.20911580.158332283386
2.5-2.630.18391790.163132043383
2.63-2.80.19471680.171532123380
2.8-3.010.18531750.167932063381
3.01-3.320.18121710.163632203391
3.32-3.80.19221680.153832303398
3.8-4.780.15421640.13432523416
4.78-35.120.17391770.174232693446

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