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- PDB-1r6u: Crystal structure of an active fragment of human tryptophanyl-tRN... -

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Basic information

Entry
Database: PDB / ID: 1r6u
TitleCrystal structure of an active fragment of human tryptophanyl-tRNA synthetase with cytokine activity
ComponentsTryptophanyl-tRNA synthetase
KeywordsLIGASE / Class Ic tRNA synthetase / Rossmann fold catalytic domain / anticodon recognition domain / bound Trp-AMP
Function / homology
Function and homology information


tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / kinase inhibitor activity / Cytosolic tRNA aminoacylation / regulation of angiogenesis / positive regulation of protein-containing complex assembly / negative regulation of protein kinase activity / angiogenesis / translation ...tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / kinase inhibitor activity / Cytosolic tRNA aminoacylation / regulation of angiogenesis / positive regulation of protein-containing complex assembly / negative regulation of protein kinase activity / angiogenesis / translation / protein domain specific binding / negative regulation of cell population proliferation / positive regulation of gene expression / protein kinase binding / protein homodimerization activity / protein-containing complex / extracellular exosome / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Tryptophan-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) ...WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / 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 / S15/NS1, RNA-binding / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TRYPTOPHANYL-5'AMP / Tryptophan--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYang, X.-L. / Otero, F.J. / Skene, R.J. / McRee, D.E. / Ribas de Pouplana, L. / Schimmel, P.
CitationJournal: Structure / Year: 2007
Title: Functional and crystal structure analysis of active site adaptations of a potent anti-angiogenic human tRNA synthetase
Authors: Yang, X.-L. / Guo, M. / Kapoor, M. / Ewalt, K.L. / Otero, F.J. / Skene, R.J. / McRee, D.E. / Schimmel, P.
History
DepositionOct 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)101,0345
Polymers100,3162
Non-polymers7183
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-25 kcal/mol
Surface area30590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.658, 96.460, 97.132
Angle α, β, γ (deg.)90.00, 129.90, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1085-

HOH

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Components

#1: Protein Tryptophanyl-tRNA synthetase / Tryptophan-tRNA ligase / TrpRS / IFP53 / hWRS


Mass: 50158.098 Da / Num. of mol.: 2 / Mutation: S213G, Y214D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WARS / Plasmid: pET20b+ / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P23381, tryptophan-tRNA ligase
#2: Chemical ChemComp-TYM / TRYPTOPHANYL-5'AMP


Mass: 533.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24N7O8P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.41 Å3/Da / Density % sol: 48.98 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 7.02
Details: PEG MME 550, Hepes, pH 7.02, VAPOR DIFFUSION, SITTING DROP, temperature 279K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12 %PEG80001reservoir
20.1 Msodium-MES1reservoirpH6.32
310 mMHEPES1droppH7.5
420 mM1dropKCl
50.02 %1dropNaN3
62 mMbeta-mercaptoethanol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 22, 2002
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91162 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 127115 / Num. obs: 126480 / % possible obs: 99.5 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.038 / Rsym value: 0.038 / Net I/σ(I): 34.7
Reflection shellResolution: 2→2.07 Å / % possible all: 99.5
Reflection
*PLUS
Num. obs: 64590
Reflection shell
*PLUS
% possible obs: 99.6 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 2

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Processing

Software
NameClassification
Blu-Icedata collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: model derived from the structure of the full-length human TrpRS

Resolution: 2→30 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2975 5859 Random
Rwork0.2535 --
all0.2548 126754 -
obs0.2548 118345 -
Solvent computationBsol: 54.3854 Å2 / ksol: 0.360966 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.342 Å20 Å21.336 Å2
2---6.463 Å20 Å2
3---0.121 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6056 0 49 100 6205
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna.param
X-RAY DIFFRACTION3WPA.param
X-RAY DIFFRACTION4goln.param
X-RAY DIFFRACTION5water_rep.param
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3

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