6D65

Crystal structure of the human dual specificity phosphatase 1 catalytic domain (C258S) as a maltose binding protein fusion in complex with the designed AR protein off7

PDB DOI: https://doi.org/10.2210/pdb6D65/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.241
R-Value Work: 0.185
R-Value Observed: 0.188

wwPDB Validation 3D Report Full Report

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

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 Search on PubMedSearch on PubMed Central
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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 154.55 kDa
Atom Count: 11,049
Modelled Residue Count: 1,333
Deposited Residue Count: 1,378
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein,Dual specificity protein phosphatase 1	A, C	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P28562P0AEX9
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Designed AR protein off7	B, D	169	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain H [auth A] SDF format, chain HA [auth C] SDF format, chain I [auth A] SDF format, chain IA [auth C] SDF format, chain J [auth A] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain R [auth A] SDF format, chain W [auth A] SDF format, chain X [auth B] SDF format, chain XA [auth D] SDF format, chain Y [auth B] SDF format, chain YA [auth D] SDF format, chain Z [auth B] SDF format, chain ZA [auth D] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain R [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth D] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth D]	CA [auth C] DA [auth C] EA [auth C] FA [auth C] GA [auth C] CA [auth C], DA [auth C], EA [auth C], FA [auth C], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], M [auth A], R [auth A], W [auth A], X [auth B], XA [auth D], Y [auth B], YA [auth D], Z [auth B], ZA [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain R [auth A] Focus chain W [auth A] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain R [auth A] Focus chain W [auth A] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain OA [auth C] SDF format, chain S [auth A] SDF format, chain WA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain WA [auth C]	E [auth A] F [auth A] G [auth A] OA [auth C] S [auth A] E [auth A], F [auth A], G [auth A], OA [auth C], S [auth A], WA [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain OA [auth C] Focus chain S [auth A] Focus chain WA [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain OA [auth C] Focus chain S [auth A] Focus chain WA [auth C]
EOH Query on EOH Download Ideal Coordinates CCD File SDF format, chain AB [auth D] SDF format, chain RA [auth C] SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain BB [auth D] SDF format, chain LA [auth C] SDF format, chain MA [auth C] SDF format, chain N [auth A] SDF format, chain NA [auth C] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain PA [auth C] SDF format, chain Q [auth A] SDF format, chain QA [auth C] SDF format, chain SA [auth C] SDF format, chain T [auth A] SDF format, chain TA [auth C] SDF format, chain U [auth A] SDF format, chain UA [auth C] SDF format, chain V [auth A] SDF format, chain VA [auth C] MOL2 format, chain AB [auth D] MOL2 format, chain RA [auth C] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth D] MOL2 format, chain LA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth C] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth C] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth C]	AA [auth B] AB [auth D] BA [auth B] BB [auth D] LA [auth C] AA [auth B], AB [auth D], BA [auth B], BB [auth D], LA [auth C], MA [auth C], N [auth A], NA [auth C], O [auth A], P [auth A], PA [auth C], Q [auth A], QA [auth C], RA [auth C], SA [auth C], T [auth A], TA [auth C], U [auth A], UA [auth C], V [auth A], VA [auth C]	ETHANOL C₂ H₆ O LFQSCWFLJHTTHZ-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain T [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain UA [auth C] Focus chain V [auth A] Focus chain VA [auth C] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain T [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain UA [auth C] Focus chain V [auth A] Focus chain VA [auth C]