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- PDB-1ntg: Crystal Structure of the EMAP II-like Cytokine Released from huma... -

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Basic information

Entry
Database: PDB / ID: 1ntg
TitleCrystal Structure of the EMAP II-like Cytokine Released from human tyrosyl-tRNA Synthetase
ComponentsTyrosyl-tRNA synthetase
KeywordsLIGASE / beta barrel
Function / homology
Function and homology information


interleukin-8 receptor binding / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / Cytosolic tRNA aminoacylation / response to starvation / small molecule binding / tRNA binding / nuclear body / apoptotic process ...interleukin-8 receptor binding / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / Cytosolic tRNA aminoacylation / response to starvation / small molecule binding / tRNA binding / nuclear body / apoptotic process / extracellular space / RNA binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Tyrosine-tRNA ligase / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Nucleic acid-binding proteins / Rossmann-like alpha/beta/alpha sandwich fold / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...: / Tyrosine-tRNA ligase / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Nucleic acid-binding proteins / Rossmann-like alpha/beta/alpha sandwich fold / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Tyrosine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsYang, X.-L. / Skene, R.J. / Mcree, D.E. / Schimmel, P.
CitationJournal: Helv.Chim.Acta / Year: 2003
Title: Crystal Structure of an EMAP-II-like Cytokine Released from a human tRNA Synthetase
Authors: Yang, X.-L. / Liu, J. / Skene, R.J. / McRee, D.E. / Schimmel, P.
History
DepositionJan 29, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name
Revision 1.5Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosyl-tRNA synthetase
B: Tyrosyl-tRNA synthetase
C: Tyrosyl-tRNA synthetase
D: Tyrosyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)76,4964
Polymers76,4964
Non-polymers00
Water3,279182
1
A: Tyrosyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)19,1241
Polymers19,1241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)19,1241
Polymers19,1241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tyrosyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)19,1241
Polymers19,1241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tyrosyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)19,1241
Polymers19,1241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.621, 59.515, 71.591
Angle α, β, γ (deg.)103.51, 109.95, 101.52
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Tyrosyl-tRNA synthetase / TyrRS


Mass: 19124.049 Da / Num. of mol.: 4 / Fragment: C-TyrRS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YARS / Plasmid: PET20b / Production host: Escherichia coli (E. coli) / References: UniProt: P54577, tyrosine-tRNA ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.63 Å3/Da / Density % sol: 52.85 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: ammonium sulfate, Sodium phosphate mono-basic, potassium phosphate di-basic, acetone, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 279K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.8 Mammonium sulfate1reservoir
20.1 Msodium potassium phosphate1reservoirpH6.9
32 %acetone1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Oct 30, 2001
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.21→20 Å / Num. all: 39281 / Num. obs: 39281 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.067
Reflection shellResolution: 2.21→2.29 Å / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 3.8 / % possible all: 83.7
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å
Reflection shell
*PLUS
% possible obs: 83.7 %

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Processing

Software
NameClassification
CNSrefinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: EMAP II structure (PDB 1FL0)

1fl0


Resolution: 2.21→20 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.296 1786 RANDOM
Rwork0.251 --
all-39761 -
obs-35773 -
Refinement stepCycle: LAST / Resolution: 2.21→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5320 0 0 182 5502
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.54
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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