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- PDB-4rrq: K121M mutant of N-terminal editing domain of threonyl-tRNA synthe... -

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Basic information

Entry
Database: PDB / ID: 4rrq
TitleK121M mutant of N-terminal editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi with L-Ser3AA
ComponentsThreonine--tRNA ligase
KeywordsLIGASE / DTD-like fold / Proofreading
Function / homologyAminoacyl-tRNA synthetase, class II / D-aminoacyl-tRNA deacylase-like superfamily / Aminoacyl-transfer RNA synthetases class-II family profile. / Archaea-specific editing domain of threonyl-tRNA synthetase / Anticodon binding domain / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding domain superfamily / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / Threonine-tRNA ligase, class IIa / Anticodon-binding ...Aminoacyl-tRNA synthetase, class II / D-aminoacyl-tRNA deacylase-like superfamily / Aminoacyl-transfer RNA synthetases class-II family profile. / Archaea-specific editing domain of threonyl-tRNA synthetase / Anticodon binding domain / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding domain superfamily / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / Threonine-tRNA ligase, class IIa / Anticodon-binding / Threonine-tRNA ligase catalytic core domain / Threonyl-tRNA synthetase, editing domain, archaea / threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / tRNA binding / zinc ion binding / ATP binding / cytoplasm / Threonine--tRNA ligase
Function and homology information
Specimen sourcePyrococcus abyssi GE5 (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 1.79 Å resolution
AuthorsHussain, T. / Kamarthapu, V. / Sankaranarayanan, R.
CitationJournal: Nat Commun / Year: 2015
Title: Specificity and catalysis hardwired at the RNA-protein interface in a translational proofreading enzyme.
Authors: Ahmad, S. / Muthukumar, S. / Kuncha, S.K. / Routh, S.B. / Yerabham, A.S. / Hussain, T. / Kamarthapu, V. / Kruparani, S.P. / Sankaranarayanan, R.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 6, 2014 / Release: Jul 15, 2015
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 15, 2015Structure modelrepositoryInitial release
1.1Nov 22, 2017Structure modelRefinement descriptionsoftware_software.classification / _software.name / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Threonine--tRNA ligase
B: Threonine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1874
Polyers33,4812
Non-polymers7072
Water5,062281
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)1960
ΔGint (kcal/M)-11
Surface area (Å2)13190
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)40.584, 74.589, 96.309
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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Components

#1: Protein/peptide Threonine--tRNA ligase / Threonyl-tRNA synthetase / ThrRS


Mass: 16740.328 Da / Num. of mol.: 2 / Fragment: UNP residues 1-147 / Mutation: K121M / Source: (gene. exp.) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / Gene: thrS, PYRAB13430, PAB1490 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UZ14, threonine-tRNA ligase
#2: Chemical ChemComp-A3S / SERINE-3'-AMINOADENOSINE / N'-L-SERYL-3'-AMINO-(3'-DEOXY)-ADENOSINE


Mass: 353.334 Da / Num. of mol.: 2 / Formula: C13H19N7O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.18 / Density percent sol: 43.69 %
Crystal growTemp: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: BisTris, NaCl, PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Collection date: Jun 15, 2009
RadiationMonochromator: Mirrors / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionD resolution high: 1.79 Å / D resolution low: 25 Å / Number all: 28360 / Number obs: 27566 / Observed criterion sigma F: 2 / Observed criterion sigma I: 2 / Percent possible obs: 97.2

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Processing

Software
NameVersionClassification
AUTOMARdata collection
MOLREPphasing
PHASERphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefineMethod to determine structure: MOLECULAR REPLACEMENT / R Free selection details: RANDOM / Sigma F: 2
Least-squares processR factor R free: 0.24 / R factor R work: 0.21 / R factor all: 0.24 / R factor obs: 0.21 / Highest resolution: 1.79 Å / Lowest resolution: 25 Å / Number reflection R free: 1377 / Number reflection all: 28360 / Number reflection obs: 27566
Refine hist #LASTHighest resolution: 1.79 Å / Lowest resolution: 25 Å
Number of atoms included #LASTProtein: 2224 / Nucleic acid: 0 / Ligand: 50 / Solvent: 281 / Total: 2555

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