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- PDB-1x8x: Tyrosyl t-RNA Synthetase from E.coli Complexed with Tyrosine -

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Basic information

Entry
Database: PDB / ID: 1x8x
TitleTyrosyl t-RNA Synthetase from E.coli Complexed with Tyrosine
ComponentsTyrosyl-tRNA synthetase
KeywordsLIGASE / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


tRNA aminoacylation / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / protein homodimerization activity / RNA binding / ATP binding / membrane / cytosol
Similarity search - Function
Tyrosine-tRNA ligase, bacterial-type, type 1 / Tyrosine-tRNA ligase, bacterial-type / Tyrosine-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 ...Tyrosine-tRNA ligase, bacterial-type, type 1 / Tyrosine-tRNA ligase, bacterial-type / Tyrosine-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 / S4 RNA-binding domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / S4 domain / S4 RNA-binding domain profile. / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TYROSINE / Tyrosine--tRNA ligase / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKobayashi, T. / Takimura, T. / Sekine, R. / Kelly, V.P. / Kamata, K. / Sakamoto, K. / Nishimura, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.MOL.BIOL. / Year: 2005
Title: Structural Snapshots of the KMSKS Loop Rearrangement for Amino Acid Activation by Bacterial Tyrosyl-tRNA Synthetase
Authors: Kobayashi, T. / Takimura, T. / Sekine, R. / Kelly, V.P. / Kamata, K. / Sakamoto, K. / Nishimura, S. / Yokoyama, S.
History
DepositionAug 19, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 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: Tyrosyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3513
Polymers36,0741
Non-polymers2772
Water3,927218
1
A: Tyrosyl-tRNA synthetase
hetero molecules

A: Tyrosyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7026
Polymers72,1482
Non-polymers5554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3370 Å2
ΔGint-46 kcal/mol
Surface area28180 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)82.820, 82.820, 93.490
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe second part of the biological assembly is generated by the two fold axis: +y, +x, -z

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Components

#1: Protein Tyrosyl-tRNA synthetase / Tyrosyl-Transfer RNA Synthetase / Tyrosine--tRNA ligase / TyrRS


Mass: 36073.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P00951, UniProt: P0AGJ9*PLUS, tyrosine-tRNA ligase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TYR / TYROSINE / Tyrosine


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.6 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulfate, PEG400, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32B2 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→71.726 Å / Num. all: 25571 / Num. obs: 25543 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 14.2 Å2 / Rsym value: 0.056 / Net I/σ(I): 8.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 3686 / Rsym value: 0.171 / % possible all: 100

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Processing

Software
NameVersionClassification
CNX2002refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNX2002phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→41.41 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1727040.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2493 9.8 %RANDOM
Rwork0.191 ---
all0.195 25509 --
obs0.194 25334 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.425 Å2 / ksol: 0.373567 e/Å3
Displacement parametersBiso mean: 23.7 Å2
Baniso -1Baniso -2Baniso -3
1-3.02 Å22.57 Å20 Å2
2--3.02 Å20 Å2
3----6.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å-0.03 Å
Refinement stepCycle: LAST / Resolution: 2→41.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2544 0 18 218 2780
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it1.912
X-RAY DIFFRACTIONc_scbond_it2.252
X-RAY DIFFRACTIONc_scangle_it3.362.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.216 394 9.5 %
Rwork0.179 3736 -
obs-4130 98.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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