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- PDB-1ulh: A short peptide insertion crucial for angiostatic activity of hum... -

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Basic information

Entry
Database: PDB / ID: 1ulh
TitleA short peptide insertion crucial for angiostatic activity of human tryptophanyl-tRNA synthetase
ComponentsTryptophanyl-tRNA synthetase
KeywordsLIGASE / aminoacylation / angiostatic cytokine / apoptosis / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
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
Tryptophan--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.31 Å
AuthorsKise, Y. / Sengoku, T. / Ishii, R. / Yokoyama, S. / Park, S.G. / Lee, S.W. / Kim, S. / Nureki, O. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: A short peptide insertion crucial for angiostatic activity of human tryptophanyl-tRNA synthetase
Authors: Kise, Y. / Lee, S.W. / Park, S.G. / Fukai, S. / Sengoku, T. / Ishii, R. / Yokoyama, S. / Kim, S. / Nureki, O.
History
DepositionSep 12, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)89,5842
Polymers89,5842
Non-polymers00
Water8,593477
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-20 kcal/mol
Surface area30330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.025, 96.606, 98.319
Angle α, β, γ (deg.)90.00, 130.26, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 44791.934 Da / Num. of mol.: 2 / Fragment: residues 35-424
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: trps / Plasmid: pET26b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P23381, tryptophan-tRNA ligase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 2.71 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 10000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
210 mMTris-HCl1droppH7.4
350 mM1dropNaCl
41 mMdithiothreitol1drop
5100 mMBis-Tris1reservoirpH5.5
680-100 mMammonium acetate1reservoir
78-12 %(w/v)PEG100001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9799 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 9, 2002 / Details: mirror
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9799 Å / Relative weight: 1
ReflectionResolution: 2.31→50 Å / Num. all: 277220 / Num. obs: 106623 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 34.1 Å2 / Rsym value: 0.056
Reflection shellResolution: 2.31→50 Å / Rsym value: 0.215 / % possible all: 76.4
Reflection
*PLUS
Lowest resolution: 50 Å / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 76.4 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.31→42.89 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1552705 / 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
Rfree0.292 1939 5 %RANDOM
Rwork0.241 ---
all0.275 40435 --
obs0.241 38685 90.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.6502 Å2 / ksol: 0.333583 e/Å3
Displacement parametersBiso mean: 53.4 Å2
Baniso -1Baniso -2Baniso -3
1--9.24 Å20 Å2-0.08 Å2
2--10.46 Å20 Å2
3----1.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.31→42.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6011 0 0 477 6488
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.021
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d1.15
LS refinement shellResolution: 2.31→2.45 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.36 265 4.7 %
Rwork0.337 5332 -
obs--79.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rwork: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.073
X-RAY DIFFRACTIONc_angle_deg1.41
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.51
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9

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