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

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Basic information

Entry
Database: PDB / ID: 8dqh
TitleCrystal structure of pyrrolysyl-tRNA synthetase from Methanomethylophilus alvus engineered for acridone amino acid (RS1) bound to ATP and acridone after 24 hours 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 / 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
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: 1.52 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

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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)62,99912
Polymers61,3822
Non-polymers1,61710
Water8,395466
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7300 Å2
ΔGint-72 kcal/mol
Surface area22400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.862, 110.862, 113.556
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: 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, 476 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#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


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


Mass: 18.015 Da / Num. of mol.: 466 / 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: 56.72 %
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: 1.52→45.44 Å / Num. obs: 105102 / % possible obs: 100 % / Redundancy: 14.2 % / Biso Wilson estimate: 23.66 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.02 / Rrim(I) all: 0.074 / Net I/σ(I): 20.4 / Num. measured all: 1496426 / Scaling rejects: 2
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
1.52-1.5514.12.8027263051610.3590.7742.9071100
8.33-45.4413.10.03686956630.9990.010.03769.498.7

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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: 1.52→45.44 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.177 5215 4.96 %
Rwork0.1652 99881 -
obs0.1658 105096 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.66 Å2 / Biso mean: 35.5107 Å2 / Biso min: 15.74 Å2
Refinement stepCycle: final / Resolution: 1.52→45.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4065 0 153 466 4684
Biso mean--39.74 36.81 -
Num. residues----530
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
1.52-1.540.35341640.31433823546
1.54-1.560.3251750.282232563431
1.56-1.570.31031820.276433223504
1.57-1.590.30481730.25632843457
1.59-1.620.2391840.250633463530
1.62-1.640.33841540.312633263480
1.64-1.660.3581790.292832983477
1.66-1.690.29581930.262933403533
1.69-1.710.25611600.234432973457
1.71-1.740.23751800.206333223502
1.74-1.770.22341690.190933453514
1.77-1.80.19921810.174533163497
1.8-1.840.19791720.169933083480
1.84-1.870.19241590.163233313490
1.87-1.920.2071670.16833353502
1.92-1.960.18391760.170933473523
1.96-2.010.18521740.174633163490
2.01-2.060.17841820.160833273509
2.06-2.120.17081620.150132873449
2.12-2.190.17981850.152233333518
2.19-2.270.15631820.145933463528
2.27-2.360.17721700.145833553525
2.36-2.470.1591790.14833023481
2.47-2.60.17651750.148933423517
2.6-2.760.15891660.158333303496
2.76-2.970.16081780.164633353513
2.98-3.270.15991760.155733283504
3.27-3.750.14331700.149633723542
3.75-4.720.14381710.134433493520
4.72-45.440.17881770.179734043581

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