6WGM

Crystal structure of a marine metagenome TRAP solute binding protein specific for pyroglutamate (Sorcerer II Global Ocean Sampling Expedition, unidentified microbe, scf7180008839099) in complex with co-purified pyroglutamate

• PDB DOI: https://doi.org/10.2210/pdb6WGM/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): uncultured bacterium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-04-05 Released: 2020-04-29 
• Deposition Author(s): Fedorov, E., Vetting, M.W., Hogle, S.L., Dupont, C.L., Almo, S.C., Ghosh, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.168 
• R-Value Work: 0.151 
• R-Value Observed: 0.152 

Starting Model: experimental

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 5IGA 5IZZ 5I5P 5I7I

Literature

Crystal structure of a marine metagenome TRAP solute binding protein specific for aromatic acid ligands (Sorcerer II Global Ocean Sampling Expedition, unidentified microbe, GOS_140), in complex with co-purified pyroglutamate

Vetting, M.W., Fedorov, E., Hogle, S.L., Dupont, C.L., Almo, S.C., Ghosh, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 36.37 kDa 
• Atom Count: 2,742 
• Modelled Residue Count: 304 
• Deposited Residue Count: 323 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRAP-type C4-dicarboxylate transport system, periplasmic component	A	323	uncultured bacterium	Mutation(s): 0  Gene Names: HIMB100_00003270
UniProt
Find proteins for G5ZWD6 (SAR116 cluster alpha proteobacterium HIMB100) Explore G5ZWD6  Go to UniProtKB:  G5ZWD6

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PCA (Subject of Investigation/LOI)	B [auth A]	PYROGLUTAMIC ACID C5 H7 N O3 ODHCTXKNWHHXJC-VKHMYHEASA-N
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT	J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL	I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.168 
• R-Value Work: 0.151 
• R-Value Observed: 0.152 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.251	α = 90
b = 56.251	β = 90
c = 193.919	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-04-29 
Deposition Author(s): Fedorov, E., Vetting, M.W., Hogle, S.L., Dupont, C.L., Almo, S.C., Ghosh, A.

Revision History  

• Version 1.0: 2020-04-29
  Type: Initial release
  
• Version 1.1: 2020-05-13
  Changes: Structure summary
• Version 1.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description