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

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Basic information

Entry
Database: PDB / ID: 2hkz
TitleCrystal structure of the editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi in complex with L-serine
ComponentsThreonyl-tRNA synthetase
KeywordsLIGASE / translation / editing / aminoacyl-tRNA synthetase / enzyme mechanism / enantioselectivity
Function / homology
Function and homology information


threonyl-tRNA aminoacylation / threonine-tRNA ligase / threonine-tRNA ligase activity / tRNA binding / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
Threonyl-tRNA synthetase, editing domain, archaea / Archaea-specific editing domain of threonyl-tRNA synthetase / D-tyrosyl-tRNA(Tyr) deacylase / D-aminoacyl-tRNA deacylase-like superfamily / Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / : / D-tyrosyl-trna(Tyr) Deacylase; Chain: A; / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) ...Threonyl-tRNA synthetase, editing domain, archaea / Archaea-specific editing domain of threonyl-tRNA synthetase / D-tyrosyl-tRNA(Tyr) deacylase / D-aminoacyl-tRNA deacylase-like superfamily / Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / : / D-tyrosyl-trna(Tyr) Deacylase; Chain: A; / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / 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) / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SERINE / Threonine--tRNA ligase
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDwivedi, S. / Kruparani, S.P. / 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.
History
DepositionJul 6, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Threonyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3872
Polymers16,2821
Non-polymers1051
Water1,910106
1
A: Threonyl-tRNA synthetase
hetero molecules

A: Threonyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7744
Polymers32,5642
Non-polymers2102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
Unit cell
Length a, b, c (Å)61.906, 61.906, 64.607
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is a dimer

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Components

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


Mass: 16281.795 Da / Num. of mol.: 1 / Fragment: editing domain (residues 1-143)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9UZ14, threonine-tRNA ligase
#2: Chemical ChemComp-SER / SERINE / Serine


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

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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: 2.19 Å3/Da / Density % sol: 43.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% PEG 8000, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 19, 2004 / Details: Osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. all: 8413 / Num. obs: 8413 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.77
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 1.85 / Num. unique all: 719 / % possible all: 84.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4(MOLREP)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Y2Q

1y2q


Resolution: 2.1→24.76 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 1299462.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.286 441 5.3 %RANDOM
Rwork0.22 ---
obs0.22 8399 96.6 %-
all-8399 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.3287 Å2 / ksol: 0.356652 e/Å3
Displacement parametersBiso mean: 30.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.85 Å2-1.09 Å20 Å2
2---2.85 Å20 Å2
3---5.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.1→24.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1140 0 7 106 1253
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.69
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.318 78 6.4 %
Rwork0.274 1147 -
obs--85.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3lsn_new.paramlsn_new.top

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