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- PDB-4rri: K116M mutant of N-terminal editing domain of threonyl-tRNA synthe... -

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Basic information

Entry
Database: PDB / ID: 4rri
TitleK116M mutant of N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Thr3AA
ComponentsProbable threonine--tRNA ligase 2
KeywordsLIGASE / DTD-like fold / Proofreading
Function / homology
Function and homology information


threonine-tRNA ligase activity / threonyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / tRNA binding / zinc ion binding / ATP binding / cytoplasm
Anticodon-binding / Threonine-tRNA ligase, class IIa / Threonyl-tRNA synthetase, editing domain, archaea / D-aminoacyl-tRNA deacylase-like superfamily / Anticodon-binding domain superfamily / Anticodon binding domain / Archaea-specific editing domain of threonyl-tRNA synthetase
Threonine--tRNA ligase editing subunit
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsAhmad, S. / Muthukumar, S. / 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
History
DepositionNov 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.name / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable threonine--tRNA ligase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5293
Polymers15,1371
Non-polymers3922
Water1,802100
1
A: Probable threonine--tRNA ligase 2
hetero molecules

A: Probable threonine--tRNA ligase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0586
Polymers30,2752
Non-polymers7834
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area2090 Å2
ΔGint-5 kcal/mol
Surface area11960 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)47.119, 47.119, 113.124
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-676-

HOH

21A-700-

HOH

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Components

#1: Protein/peptide Probable threonine--tRNA ligase 2 / Threonyl-tRNA synthetase 2 / ThrRS 2


Mass: 15137.429 Da / Num. of mol.: 1 / Fragment: UNP residues 1-136 / Mutation: K116M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea)
Strain: ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1
Gene: thrS2, APE_0117.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9YFY3, threonine-tRNA ligase
#2: Chemical ChemComp-A3T / 3'-deoxy-3'-(L-threonylamino)adenosine


Mass: 367.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H21N7O5
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Magnesium
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / 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: 2.07 Å3/Da / Density % sol: 40.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris HCl pH 8.5, 0.2M MgCl2, 30% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 15, 2012
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→25 Å / Num. all: 20109 / Num. obs: 19968 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→25 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.65 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.105 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1083 5.1 %RANDOM
Rwork0.191 ---
Obs0.195 19968 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1067 0 27 100 1194
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0180.021123
r_bond_other_d
r_angle_refined_deg1.9431.9971529
r_angle_other_deg
r_dihedral_angle_1_deg6.4215135
r_dihedral_angle_2_deg43.00121.59144
r_dihedral_angle_3_deg14.20815173
r_dihedral_angle_4_deg10.671158
r_chiral_restr0.120.2168
r_gen_planes_refined0.0120.022853
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr6.08831123
r_sphericity_free30.342534
r_sphericity_bonded16.28351157
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.515 70 -
Rwork0.402 1237 -
Obs--96.17 %

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