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- PDB-3jxe: Crystal structure of Pyrococcus horikoshii tryptophanyl-tRNA synt... -

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Basic information

Entry
Database: PDB / ID: 3jxe
TitleCrystal structure of Pyrococcus horikoshii tryptophanyl-tRNA synthetase in complex with TrpAMP
ComponentsTryptophanyl-tRNA synthetase
KeywordsLIGASE / tryptophanyl-tRNA synthetase / Adenosine Triphosphate / Rossmann fold / P. horikoshii / Aminoacyl-tRNA synthetase / ATP-binding / Cytoplasm / Nucleotide-binding / Protein biosynthesis
Function / homology
Function and homology information


tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / ATP binding / cytoplasm
Similarity search - Function
Tryptophan-tRNA ligase, archaea / Tryptophan-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold ...Tryptophan-tRNA ligase, archaea / Tryptophan-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TRYPTOPHANYL-5'AMP / Tryptophan--tRNA ligase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsZhou, M. / Dong, X. / Zhong, C. / Shen, N. / Yang, B. / Ding, J.
CitationJournal: To be Published
Title: Crystal structure of P. horikoshii tryptophanyl-tRNA synthetase and structure-based phylogenetic analysis suggest an archaeal origin of tryptophanyl-tRNA synthetase
Authors: Zhou, M. / Dong, X. / Zhong, C. / Shen, N. / Yang, B. / Ding, J.
History
DepositionSep 19, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)93,6636
Polymers92,4042
Non-polymers1,2594
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-67 kcal/mol
Surface area29870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.198, 170.198, 170.198
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Tryptophanyl-tRNA synthetase / Tryptophan-tRNA ligase / TrpRS


Mass: 46202.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH1921, trpS / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O59584, tryptophan-tRNA ligase
#2: Chemical ChemComp-TYM / TRYPTOPHANYL-5'AMP


Mass: 533.431 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H24N7O8P
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 4.45 Å3/Da / Density % sol: 72.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 0.1M sodium citrate, 1.6M (NH4)2SO4, 10mM MnCl2, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 33131 / % possible obs: 100 % / Redundancy: 15.5 % / Biso Wilson estimate: 99.3 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 33.1
Reflection shellResolution: 3→3.11 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.788 / Mean I/σ(I) obs: 2.6 / Num. unique all: 3255 / % possible all: 99.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.905 / Occupancy max: 1 / Occupancy min: 0.7 / SU B: 15.764 / SU ML: 0.276 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.684 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1650 5 %RANDOM
Rwork0.238 ---
obs0.239 33089 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.59 Å2 / Biso mean: 79.725 Å2 / Biso min: 41.91 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6035 0 84 12 6131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226292
X-RAY DIFFRACTIONr_angle_refined_deg0.9851.9748482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.775720
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.25223.826298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.929151146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.441530
X-RAY DIFFRACTIONr_chiral_restr0.0710.2883
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024716
X-RAY DIFFRACTIONr_nbd_refined0.1780.23078
X-RAY DIFFRACTIONr_nbtor_refined0.3030.24320
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2165
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.25
X-RAY DIFFRACTIONr_mcbond_it0.351.53732
X-RAY DIFFRACTIONr_mcangle_it0.54725872
X-RAY DIFFRACTIONr_scbond_it0.5532961
X-RAY DIFFRACTIONr_scangle_it0.7724.52610
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 115 -
Rwork0.384 2293 -
all-2408 -
obs--99.26 %

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