6D66

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

PDB DOI: https://doi.org/10.2210/pdb6D66/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., Waugh, D.S., Lountos, G.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.23 Å
R-Value Free: 0.202
R-Value Work: 0.159
R-Value Observed: 0.162

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: 74.01 kDa
Atom Count: 5,428
Modelled Residue Count: 642
Deposited Residue Count: 656
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	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 mbp3_16	B	136	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A]	J [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth A] SDF format, chain Q [auth A] MOL2 format, chain F [auth A] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth A]	F [auth A], M [auth A], Q [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain M [auth A] Focus chain Q [auth A] Interactions & Density Focus chain F [auth A] Focus chain M [auth A] Focus chain Q [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain S [auth A] SDF format, chain X [auth B] MOL2 format, chain C [auth A] MOL2 format, chain S [auth A] MOL2 format, chain X [auth B]	C [auth A], S [auth A], X [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain S [auth A] Focus chain X [auth B] Interactions & Density Focus chain C [auth A] Focus chain S [auth A] Focus chain X [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
DAL Query on DAL Download Ideal Coordinates CCD File SDF format, chain Y [auth B] MOL2 format, chain Y [auth B]	Y [auth B]	D-ALANINE C₃ H₇ N O₂ QNAYBMKLOCPYGJ-UWTATZPHSA-N		Interactions Focus chain Y [auth B] Interactions & Density Focus chain Y [auth B]
GLY Query on GLY Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] MOL2 format, chain E [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A]	E [auth A], N [auth A], O [auth A]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain E [auth A] Focus chain N [auth A] Focus chain O [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain P [auth A] SDF format, chain R [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain Z [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain P [auth A] MOL2 format, chain R [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain Z [auth B]	G [auth A] H [auth A] I [auth A] K [auth A] L [auth A] G [auth A], H [auth A], I [auth A], K [auth A], L [auth A], P [auth A], R [auth A], T [auth A], U [auth A], V [auth B], W [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth A] Focus chain R [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain Z [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth A] Focus chain R [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain Z [auth B]