6D67

Crystal structure of the human dual specificity phosphatase 1 catalytic domain (C258S) as a maltose binding protein fusion (maltose bound form) in complex with the designed AR protein mbp3_16

• PDB DOI: https://doi.org/10.2210/pdb6D67/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12, Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-04-20 Released: 2018-09-19 
• Deposition Author(s): Gumpena, R., Lountos, G.T., Waugh, D.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.252 
• R-Value Work: 0.182 
• R-Value Observed: 0.185 

Literature

MBP-binding DARPins facilitate the crystallization of an MBP fusion protein.

Gumpena, R., Lountos, G.T., Waugh, D.S.

(2018) Acta Crystallogr F Struct Biol Commun 74: 549-557

• PubMed: 30198887 
• DOI: https://doi.org/10.1107/S2053230X18009901
• Primary Citation of Related Structures:  
  6D65, 6D66, 6D67


• PubMed Abstract: 
  

  The production of high-quality crystals is the main bottleneck in determining the structures of proteins using X-ray crystallography. In addition to being recognized as a very effective solubility-enhancing fusion partner, Escherichia coli maltose-binding protein (MBP) has also been successfully employed as a `fixed-arm' crystallization chaperone in more than 100 cases. Here, it is reported that designed ankyrin-repeat proteins (DARPins) that bind with high affinity to MBP can promote the crystallization of an MBP fusion protein when the fusion protein alone fails to produce diffraction-quality crystals. As a proof of principle, three different co-crystal structures of MBP fused to the catalytic domain of human dual-specificity phosphatase 1 in complex with DARPins are reported.

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Organizational Affiliation: 

Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 72.62 kDa 
• Atom Count: 5,026 
• Modelled Residue Count: 642 
• Deposited Residue Count: 656 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein,Dual specificity protein phosphatase 1	A	520	Escherichia coli K-12, Homo sapiens This entity is chimeric	Mutation(s): 9  Gene Names: malE, b4034, JW3994, DUSP1, CL100, MKP1, PTPN10, VH1 EC: 3.1.3.16 (PDB Primary Data), 3.1.3.48 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
Find proteins for P28562 (Homo sapiens) Explore P28562  Go to UniProtKB:  P28562
PHAROS:  P28562 GTEx:  ENSG00000120129
UniProt Groups	P28562P0AEX9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Designed AR protein mbp3_16	B	136	synthetic construct	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C	2		N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4	E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	F [auth A], G [auth A], H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	C	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.252 
• R-Value Work: 0.182 
• R-Value Observed: 0.185 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.286	α = 90
b = 84.699	β = 90
c = 105.962	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-09-19 
Deposition Author(s): Gumpena, R., Lountos, G.T., Waugh, D.S.

Revision History  

• Version 1.0: 2018-09-19
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary