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- PDB-2cyb: Crystal structure of Tyrosyl-tRNA Synthetase complexed with L-tyr... -

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Basic information

Entry
Database: PDB / ID: 2cyb
TitleCrystal structure of Tyrosyl-tRNA Synthetase complexed with L-tyrosine from Archaeoglobus fulgidus
ComponentsTyrosyl-tRNA synthetase
KeywordsLIGASE / Rossmann-fold / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase activity / tyrosine-tRNA ligase / ATP binding / cytoplasm
Similarity search - Function
Tyrosine-tRNA ligase, type 3 / Tyrosine-tRNA ligase, archaeal/eukaryotic-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-transfer RNA synthetases class-I signature. / Aminoacyl-tRNA synthetase, class I, conserved site / HUPs ...Tyrosine-tRNA ligase, type 3 / Tyrosine-tRNA ligase, archaeal/eukaryotic-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-transfer RNA synthetases class-I signature. / Aminoacyl-tRNA synthetase, class I, conserved site / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TYROSINE / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKuratani, M. / Sakai, H. / Takahashi, M. / Yanagisawa, T. / Kobayashi, T. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structures of Tyrosyl-tRNA Synthetases from Archaea
Authors: Kuratani, M. / Sakai, H. / Takahashi, M. / Yanagisawa, T. / Kobayashi, T. / Murayama, K. / Chen, L. / Liu, Z.J. / Wang, B.C. / Kuroishi, C. / Kuramitsu, S. / Terada, T. / Bessho, Y. / ...Authors: Kuratani, M. / Sakai, H. / Takahashi, M. / Yanagisawa, T. / Kobayashi, T. / Murayama, K. / Chen, L. / Liu, Z.J. / Wang, B.C. / Kuroishi, C. / Kuramitsu, S. / Terada, T. / Bessho, Y. / Shirouzu, M. / Sekine, S. / Yokoyama, S.
History
DepositionJul 6, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)73,6994
Polymers73,3372
Non-polymers3622
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-29 kcal/mol
Surface area27620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.620, 96.158, 92.636
Angle α, β, γ (deg.)90.00, 94.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 36668.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Plasmid: pET41a / Production host: Escherichia coli (E. coli) / References: UniProt: O29482, tyrosine-tRNA ligase
#2: Chemical ChemComp-TYR / TYROSINE / Tyrosine


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.57 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Ammonium sulfate, PEG400, 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: BL41XU / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 12, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 65745 / Num. obs: 65483 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 25.8 Å2 / Rsym value: 0.051 / Net I/σ(I): 21.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.469 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→46.18 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1637216.28 / 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
Rfree0.24 3321 5.1 %RANDOM
Rwork0.202 ---
all0.203 65713 --
obs0.202 65455 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.3651 Å2 / ksol: 0.378155 e/Å3
Displacement parametersBiso mean: 37.5 Å2
Baniso -1Baniso -2Baniso -3
1-8.38 Å20 Å24.78 Å2
2---5.72 Å20 Å2
3----2.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.8→46.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5066 0 26 314 5406
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.303 552 5 %
Rwork0.272 10385 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.param&_1_TOPOLOGY_INFILE_1
X-RAY DIFFRACTION2water_rep.param&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3ion.param&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4cisAf.param&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5&_1_TOPOLOGY_INFILE_5

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