6EOK

Crystal structure of E. coli L-asparaginase II

PDB DOI: https://doi.org/10.2210/pdb6EOK/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-10-09 Released: 2018-10-31
Deposition Author(s): Cerofolini, L., Giuntini, S., Carlon, A., Ravera, E., Calderone, V., Fragai, M., Parigi, G., Luchinat, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.252
R-Value Work: 0.189
R-Value Observed: 0.193

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Characterization of PEGylated Asparaginase: New Opportunities from NMR Analysis of Large PEGylated Therapeutics.

Cerofolini, L., Giuntini, S., Carlon, A., Ravera, E., Calderone, V., Fragai, M., Parigi, G., Luchinat, C.

(2019) Chemistry 25: 1984-1991

PubMed: 30462348 Search on PubMed
DOI: https://doi.org/10.1002/chem.201804488
Primary Citation of Related Structures:
6EOK

PubMed Abstract:
Resonance assignment and structural characterization of pharmacologically relevant proteins promise to improve understanding and safety of these proteins by rational design. However, the PEG coating that is used to evade the immune system also causes these molecules to "evade" the standard structural biology methodologies. We here demonstrate that it is possible to obtain the resonance assignment and a reliable structural model of large PEGylated proteins through an integrated approach encompassing NMR and X-ray crystallography.

Organizational Affiliation

Magnetic Resonance Center (CERM), University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di, Metallo Proteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.

Macromolecule Content

Total Structure Weight: 138.77 kDa
Atom Count: 9,528
Modelled Residue Count: 1,212
Deposited Residue Count: 1,304
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-asparaginase 2	A, B, C, D	326	Escherichia coli K-12	Mutation(s): 0 Gene Names: ansB, b2957, JW2924 EC: 3.5.1.1
UniProt
Find proteins for P00805 (Escherichia coli (strain K12)) Explore P00805 Go to UniProtKB: P00805
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00805
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.252
R-Value Work: 0.189
R-Value Observed: 0.193
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.33	α = 90
b = 121.23	β = 90
c = 126.56	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2018-10-31

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-10-31
Type: Initial release
Version 1.1: 2018-12-05
Changes: Data collection, Database references
Version 1.2: 2019-02-20
Changes: Data collection, Database references
Version 1.3: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description