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- PDB-2hl2: Crystal structure of the editing domain of threonyl-tRNA syntheta... -

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Entry
Database: PDB / ID: 2hl2
TitleCrystal structure of the editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi in complex with an analog of seryladenylate
ComponentsThreonyl-tRNA synthetase
KeywordsLIGASE / translation / editing / aminoacyl-tRNA synthetase / enzyme mechanism / enantioselectivity
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 (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 2.6 Å resolution
AuthorsHussain, T. / Kruparani, S.P. / Pal, B. / Sankaranarayanan, R.
Citation
Journal: Embo J. / Year: 2006
Title: Post-transfer editing mechanism of a D-aminoacyl-tRNA deacylase-like domain in threonyl-tRNA synthetase from archaea
Authors: Hussain, T. / Kruparani, S.P. / Pal, B. / Dock-Bregeon, A.C. / Dwivedi, S. / Shekar, M.R. / Sureshbabu, K. / Sankaranarayanan, R.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2005
Title: A D-amino acid editing module coupled to the translational apparatus in archaea
Authors: Dwivedi, S. / Kruparani, S.P. / Sankaranarayanan, R.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 6, 2006 / Release: Aug 29, 2006
RevisionDateData content typeGroupProviderType
1.0Aug 29, 2006Structure modelrepositoryInitial release
1.1May 1, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Threonyl-tRNA synthetase
B: Threonyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4304
Polyers32,5642
Non-polymers8672
Water1,62190
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)39.652, 67.363, 98.588
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21
DetailsThe biological assembly is a dimer

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Components

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


Mass: 16281.795 Da / Num. of mol.: 2 / Fragment: editing domain (residues 1-143) / Source: (gene. exp.) Pyrococcus abyssi (archaea) / Genus: Pyrococcus / Plasmid name: pET21b / Genus (production host): Escherichia / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9UZ14, threonine-tRNA ligase
#2: Chemical ChemComp-SSA / 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE


Mass: 433.397 Da / Num. of mol.: 2 / Formula: C13H19N7O8S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.02 / Density percent sol: 39.13 %
Crystal growTemp: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 3350, 0.1M bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Details: Osmic mirrors / Detector: IMAGE PLATE / Collection date: Nov 6, 2005
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 63.8 Å2 / D resolution high: 2.6 Å / D resolution low: 25 Å / Number all: 8487 / Number obs: 8487 / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Rmerge I obs: 0.08 / NetI over sigmaI: 14.75 / Redundancy: 3.6 % / Percent possible obs: 97.8
Reflection shellRmerge I obs: 0.409 / Highest resolution: 2.6 Å / Lowest resolution: 2.69 Å / MeanI over sigI obs: 2.12 / Number unique all: 724 / Redundancy: 2.8 % / Percent possible all: 86.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4(MOLREP)phasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Y2Q
R Free selection details: RANDOM / Data cutoff high absF: 958280.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0 / Stereochemistry target values: Engh & Huber
Solvent computationSolvent model details: FLAT MODEL / Solvent model param bsol: 26.1338 / Solvent model param ksol: 0.287978
Displacement parametersB iso mean: 43.8 Å2 / Aniso B11: 4.47 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: -5.36 Å2 / Aniso B23: 0 Å2 / Aniso B33: 0.89 Å2
Least-squares processR factor R free: 0.295 / R factor R free error: 0.014 / R factor R work: 0.213 / R factor obs: 0.213 / Highest resolution: 2.6 Å / Lowest resolution: 24.84 Å / Number reflection R free: 438 / Number reflection all: 8432 / Number reflection obs: 8432 / Percent reflection R free: 5.2 / Percent reflection obs: 98.4
Refine analyzeLuzzati coordinate error free: 0.52 Å / Luzzati coordinate error obs: 0.35 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a free: 0.48 Å / Luzzati sigma a obs: 0.42 Å
Refine hist #LASTHighest resolution: 2.6 Å / Lowest resolution: 24.84 Å
Number of atoms included #LASTProtein: 2280 / Nucleic acid: 0 / Ligand: 58 / Solvent: 90 / Total: 2428
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.281.50
X-RAY DIFFRACTIONc_mcangle_it2.192.00
X-RAY DIFFRACTIONc_scbond_it1.962.00
X-RAY DIFFRACTIONc_scangle_it3.092.50
Refine LS shellHighest resolution: 2.6 Å / R factor R free: 0.391 / R factor R free error: 0.045 / R factor R work: 0.336 / Lowest resolution: 2.76 Å / Number reflection R free: 76 / Number reflection R work: 1225 / Total number of bins used: 6 / Percent reflection R free: 5.8 / Percent reflection obs: 94.9
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ssa.paramssa.top

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