5YZX

Crystal structure of E.coli LysU T146D mutant

  • Classification: LIGASE
  • Organism(s): Escherichia coli K-12
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2017-12-16 Released: 2018-12-19 
  • Deposition Author(s): Fang, P., Guo, M.
  • Funding Organization(s): National Institutes of Health, Shanghai Pujiang Program, National Natural Science Foundation of China

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.238 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

A proposed role for MSC to reserve the canonical function in high eukaryotes prior to stimuli

Zheng, L., Ali, H., Wang, J., Guo, M., Fang, P.

To be published.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysine--tRNA ligase, heat inducible
A, B, C
525Escherichia coli K-12Mutation(s): 1 
Gene Names: lysU, b4129, JW4090
EC: 6.1.1.6
UniProt
Find proteins for P0A8N5 (Escherichia coli (strain K12))
Explore P0A8N5 
Go to UniProtKB:  P0A8N5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A8N5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B4P
Query on B4P
Download Ideal Coordinates CCD File 
D [auth A],
H [auth B],
L [auth C]		BIS(ADENOSINE)-5'-TETRAPHOSPHATE
C20 H28 N10 O19 P4
YOAHKNVSNCMZGQ-XPWFQUROSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
I [auth B]
J [auth B]
E [auth A],
F [auth A],
G [auth A],
I [auth B],
J [auth B],
K [auth B],
M [auth C],
N [auth C],
O [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.238 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.544α = 90
b = 249.855β = 90
c = 179.652γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of HealthUnited StatesGM100136
National Institutes of HealthUnited StatesGM106134
Shanghai Pujiang ProgramChina17PJ1410800
National Natural Science Foundation of ChinaChina21778067
National Natural Science Foundation of ChinaChina21778064

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description