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- PDB-4tqd: Crystal Structure of the C-terminal domain of IFRS bound with 3-i... -

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Basic information

Entry
Database: PDB / ID: 4tqd
TitleCrystal Structure of the C-terminal domain of IFRS bound with 3-iodo-L-Phe and ATP
ComponentsPyrrolysine--tRNA ligase
KeywordsLIGASE / Amino Acyl-tRNA Synthetases / Archaeal Proteins / Evolution / Molecular / Genetic Code / Substrate Specificity
Function / homologyPhenylalanyl-tRNA synthetase / Aminoacyl-tRNA synthetase, class II / Pyrrolysyl-tRNA ligase / Pyrrolysyl-tRNA ligase, C-terminal / Pyrrolysyl-tRNA ligase, N-terminal / tRNA synthetases class II core domain (F) / Aminoacyl-transfer RNA synthetases class-II family profile. / pyrrolysine-tRNAPyl ligase / aminoacyl-tRNA ligase activity / tRNA aminoacylation for protein translation ...Phenylalanyl-tRNA synthetase / Aminoacyl-tRNA synthetase, class II / Pyrrolysyl-tRNA ligase / Pyrrolysyl-tRNA ligase, C-terminal / Pyrrolysyl-tRNA ligase, N-terminal / tRNA synthetases class II core domain (F) / Aminoacyl-transfer RNA synthetases class-II family profile. / pyrrolysine-tRNAPyl ligase / aminoacyl-tRNA ligase activity / tRNA aminoacylation for protein translation / tRNA binding / ATP binding / cytoplasm / Pyrrolysine--tRNA ligase
Function and homology information
Specimen sourceMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2.1429 Å resolution
AuthorsNakamura, A. / O'Donoghue, P. / Soll, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Polyspecific pyrrolysyl-tRNA synthetases from directed evolution.
Authors: Guo, L.T. / Wang, Y.S. / Nakamura, A. / Eiler, D. / Kavran, J.M. / Wong, M. / Kiessling, L.L. / Steitz, T.A. / O'Donoghue, P. / Soll, D.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 11, 2014 / Release: Nov 12, 2014
RevisionDateData content typeGroupProviderType
1.0Nov 12, 2014Structure modelrepositoryInitial release
1.1Nov 26, 2014Structure modelDatabase references
1.2Dec 3, 2014Structure modelDatabase references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyrrolysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,70513
Polyers33,3991
Non-polymers1,30612
Water2,126118
1
A: Pyrrolysine--tRNA ligase
hetero molecules

A: Pyrrolysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,41026
Polyers66,7982
Non-polymers2,61124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area (Å2)9830
ΔGint (kcal/M)-28
Surface area (Å2)22620
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)104.700, 104.700, 70.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP 64

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Components

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide Pyrrolysine--tRNA ligase / Pyrrolysine--tRNA(Pyl) ligase / Pyrrolysyl-tRNA synthetase / PylRS


Mass: 33399.219 Da / Num. of mol.: 1 / Mutation: N346S, C348I / Source: (gene. exp.) Methanosarcina mazei (archaea)
Strain: ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88
Gene: pylS, MM_1445 / Plasmid name: pet15b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 Codon Plus RIL (DE3) / References: UniProt: Q8PWY1, pyrrolysine-tRNAPyl ligase

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Non-polymers , 5 types, 130 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Formula: Mg / Magnesium
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#4: Chemical ChemComp-33S / 3-iodo-L-phenylalanine


Mass: 291.086 Da / Num. of mol.: 1 / Formula: C9H10INO2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Formula: C2H6O2 / Ethylene glycol
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Formula: H2O / Water

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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: 3.35 / Density percent sol: 63.26 %
Crystal growTemp: 298 K / Method: vapor diffusion, sitting drop / Details: Hepes, MgCl2, PEG3350 / PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Collection date: Apr 14, 2013
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionD resolution high: 2.14 Å / D resolution low: 42.064 Å / Number obs: 24274 / NetI over sigmaI: 34.24 / Redundancy: 20 % / Percent possible obs: 99.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZIM
Overall SU ML: 0.19 / Cross valid method: THROUGHOUT / Sigma F: 2.01 / Overall phase error: 19.91 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Least-squares processR factor R free: 0.1925 / R factor R work: 0.1551 / R factor obs: 0.1589 / Highest resolution: 2.1429 Å / Lowest resolution: 42.064 Å / Number reflection R free: 2433 / Number reflection obs: 24270 / Percent reflection R free: 10.02 / Percent reflection obs: 99.79
Refine hist #LASTHighest resolution: 2.1429 Å / Lowest resolution: 42.064 Å
Number of atoms included #LASTProtein: 2100 / Nucleic acid: 0 / Ligand: 75 / Solvent: 118 / Total: 2293
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142253
X-RAY DIFFRACTIONf_angle_d1.4503029
X-RAY DIFFRACTIONf_dihedral_angle_d17.011894
X-RAY DIFFRACTIONf_chiral_restr0.069324
X-RAY DIFFRACTIONf_plane_restr0.007387
Refine LS shell

Refine ID: X-RAY DIFFRACTION

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
2.14290.23080.18372.1866137122297.00
2.18660.25710.17802.23421261309100.00
2.23420.21410.17992.28611341286100.00
2.28610.24480.16692.34331401291100.00
2.34330.20780.16022.40661301265100.00
2.40660.22050.16842.47741461289100.00
2.47740.23810.17332.55741401284100.00
2.55740.20590.16352.64881401271100.00
2.64880.21570.16912.75481401302100.00
2.75480.21800.16592.88021591264100.00
2.88020.21250.17043.03201411290100.00
3.03200.22030.17223.22191421275100.00
3.22190.23670.17053.47051611279100.00
3.47050.20030.15573.81961371307100.00
3.81960.14520.13294.37181561283100.00
4.37180.16670.12795.50601501302100.00
5.50600.15090.149842.07171541318100.00

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