4XNJ

X-ray structure of PepTst2

PDB DOI: https://doi.org/10.2210/pdb4XNJ/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Streptococcus thermophilus LMG 18311
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMDmpstruc

Deposited: 2015-01-15 Released: 2015-06-03
Deposition Author(s): Huang, C.Y., Olieric, V., Diederichs, K., Wang, M., Caffrey, M.
Funding Organization(s): Science Foundation Ireland, National Institutes of Health

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.251
R-Value Work: 0.203
R-Value Observed: 0.205

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

In meso in situ serial X-ray crystallography of soluble and membrane proteins.

Huang, C.Y., Olieric, V., Ma, P., Panepucci, E., Diederichs, K., Wang, M., Caffrey, M.

(2015) Acta Crystallogr D Biol Crystallogr 71: 1238-1256

PubMed: 26057665 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S1399004715005210
Primary Citation of Related Structures:
4XJB, 4XJD, 4XJF, 4XJG, 4XJH, 4XJI, 4XNI, 4XNJ, 4XNK, 4XNL

PubMed Abstract:

The lipid cubic phase (LCP) continues to grow in popularity as a medium in which to generate crystals of membrane (and soluble) proteins for high-resolution X-ray crystallographic structure determination. To date, the PDB includes 227 records attributed to the LCP or in meso method. Among the listings are some of the highest profile membrane proteins, including the β2-adrenoreceptor-Gs protein complex that figured in the award of the 2012 Nobel Prize in Chemistry to Lefkowitz and Kobilka. The most successful in meso protocol to date uses glass sandwich crystallization plates. Despite their many advantages, glass plates are challenging to harvest crystals from. However, performing in situ X-ray diffraction measurements with these plates is not practical. Here, an alternative approach is described that provides many of the advantages of glass plates and is compatible with high-throughput in situ measurements. The novel in meso in situ serial crystallography (IMISX) method introduced here has been demonstrated with AlgE and PepT (alginate and peptide transporters, respectively) as model integral membrane proteins and with lysozyme as a test soluble protein. Structures were solved by molecular replacement and by experimental phasing using bromine SAD and native sulfur SAD methods to resolutions ranging from 1.8 to 2.8 Å using single-digit microgram quantities of protein. That sulfur SAD phasing worked is testament to the exceptional quality of the IMISX diffraction data. The IMISX method is compatible with readily available, inexpensive materials and equipment, is simple to implement and is compatible with high-throughput in situ serial data collection at macromolecular crystallography synchrotron beamlines worldwide. Because of its simplicity and effectiveness, the IMISX approach is likely to supplant existing in meso crystallization protocols. It should prove particularly attractive in the area of ligand screening for drug discovery and development.

Organizational Affiliation:

Membrane Structural and Functional Biology Group, Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Di-or tripeptide:H+ symporter	A	483	Streptococcus thermophilus LMG 18311	Mutation(s): 0 Gene Names: dtpT, stu0970 Membrane Entity: Yes
UniProt
Find proteins for Q5M4H8 (Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311)) Explore Q5M4H8 Go to UniProtKB: Q5M4H8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5M4H8
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
78M Query on 78M Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A]	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A]	(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE C₁₈ H₃₄ O₄ BJMLBVHMHXYQFS-JJEJIETFSA-N		Ligand Interaction
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A]	O [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Ligand Interaction