1NTG | pdb_00001ntg

Crystal Structure of the EMAP II-like Cytokine Released from human tyrosyl-tRNA Synthetase

• PDB DOI: https://doi.org/10.2210/pdb1NTG/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-01-29 Released: 2003-05-13 
• Deposition Author(s): Yang, X.-L., Skene, R.J., Mcree, D.E., Schimmel, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 
  0.296 (Depositor), 0.298 (DCC) 
• R-Value Work: 
  0.251 (Depositor), 0.250 (DCC) 

Starting Model: experimental

Literature

Crystal Structure of an EMAP-II-like Cytokine Released from a human tRNA Synthetase

Yang, X.-L., Liu, J., Skene, R.J., McRee, D.E., Schimmel, P.

(2003) Helvetica Chim Acta 86: 1246-1257

• DOI: https://doi.org/10.1002/hlca.200390107

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 76.5 kDa 
• Atom Count: 5,502 
• Modeled Residue Count: 684 
• Deposited Residue Count: 688 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosyl-tRNA synthetase	A, B, C, D	172	Homo sapiens	Mutation(s): 0  Gene Names: YARS EC: 6.1.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P54577 (Homo sapiens) Explore P54577  Go to UniProtKB:  P54577
PHAROS:  P54577 GTEx:  ENSG00000134684

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free:  0.296 (Depositor), 0.298 (DCC) 
• R-Value Work:  0.251 (Depositor), 0.250 (DCC) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.621	α = 103.51
b = 59.515	β = 109.95
c = 71.591	γ = 101.52

Software Package:

Software Name	Purpose
CNS	refinement
MAR345	data collection
SCALEPACK	data scaling
CNS	phasing
SHELXL-97	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-05-13 
Deposition Author(s): Yang, X.-L., Skene, R.J., Mcree, D.E., Schimmel, P.

Revision History  

• Version 1.0: 2003-05-13
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.5: 2023-08-16
  Changes: Data collection, Database references, Refinement description