6DG3 | pdb_00006dg3

LarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase, in complex with caesium

PDB DOI: https://doi.org/10.2210/pdb6DG3/pdb

Classification: TRANSFERASE
Organism(s): Lactiplantibacillus plantarum WCFS1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-05-16 Released: 2019-05-22
Deposition Author(s): Fellner, M., Hausinger, R.P., Hu, J.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.94 Å
R-Value Free:
0.274 (Depositor), 0.280 (DCC)
R-Value Work:
0.196 (Depositor), 0.200 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Unique cesium-binding sites in proteins, a case study with the sacrificial sulfur transferase LarE

Fellner, M.

(2021) J Life Sci (Westlake Village)

DOI: https://doi.org/10.36069/JoLS/20210305

Macromolecule Content

Total Structure Weight: 383.36 kDa
Atom Count: 21,737
Modeled Residue Count: 2,874
Deposited Residue Count: 3,432
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridinium-3,5-biscarboxylic acid mononucleotide sulfurtransferase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	286	Lactiplantibacillus plantarum WCFS1	Mutation(s): 0 Gene Names: larE, lp_0109 EC: 2.8.1 (PDB Primary Data), 4.4.1.37 (UniProt)
UniProt
Find proteins for F9UST4 (Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)) Explore F9UST4 Go to UniProtKB: F9UST4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F9UST4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CS Query on CS Download Ideal Coordinates CCD File SDF format, chain Y [auth G] SDF format, chain W [auth F] SDF format, chain U [auth E] SDF format, chain S [auth D] SDF format, chain Q [auth C] SDF format, chain O [auth B] SDF format, chain M [auth A] SDF format, chain IA [auth L] SDF format, chain GA [auth K] SDF format, chain EA [auth J] SDF format, chain CA [auth I] SDF format, chain AA [auth H] MOL2 format, chain Y [auth G] MOL2 format, chain W [auth F] MOL2 format, chain U [auth E] MOL2 format, chain S [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain O [auth B] MOL2 format, chain M [auth A] MOL2 format, chain IA [auth L] MOL2 format, chain GA [auth K] MOL2 format, chain EA [auth J] MOL2 format, chain CA [auth I] MOL2 format, chain AA [auth H] mmCIF format, chain Y [auth G] mmCIF format, chain W [auth F] mmCIF format, chain U [auth E] mmCIF format, chain S [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain O [auth B] mmCIF format, chain M [auth A] mmCIF format, chain IA [auth L] mmCIF format, chain GA [auth K] mmCIF format, chain EA [auth J] mmCIF format, chain CA [auth I] mmCIF format, chain AA [auth H]	AA [auth H] CA [auth I] EA [auth J] GA [auth K] IA [auth L] AA [auth H], CA [auth I], EA [auth J], GA [auth K], IA [auth L], M [auth A], O [auth B], Q [auth C], S [auth D], U [auth E], W [auth F], Y [auth G]	CESIUM ION Cs NCMHKCKGHRPLCM-UHFFFAOYSA-N		Interactions Focus chain AA [auth H] Focus chain CA [auth I] Focus chain EA [auth J] Focus chain GA [auth K] Focus chain IA [auth L] Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Y [auth G] Interactions & Density Focus chain AA [auth H] Focus chain CA [auth I] Focus chain EA [auth J] Focus chain GA [auth K] Focus chain IA [auth L] Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Y [auth G]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain Z [auth G] SDF format, chain X [auth F] SDF format, chain V [auth E] SDF format, chain T [auth D] SDF format, chain R [auth C] SDF format, chain P [auth B] SDF format, chain N [auth A] SDF format, chain JA [auth L] SDF format, chain HA [auth K] SDF format, chain FA [auth J] SDF format, chain DA [auth I] SDF format, chain BA [auth H] MOL2 format, chain Z [auth G] MOL2 format, chain X [auth F] MOL2 format, chain V [auth E] MOL2 format, chain T [auth D] MOL2 format, chain R [auth C] MOL2 format, chain P [auth B] MOL2 format, chain N [auth A] MOL2 format, chain JA [auth L] MOL2 format, chain HA [auth K] MOL2 format, chain FA [auth J] MOL2 format, chain DA [auth I] MOL2 format, chain BA [auth H] mmCIF format, chain Z [auth G] mmCIF format, chain X [auth F] mmCIF format, chain V [auth E] mmCIF format, chain T [auth D] mmCIF format, chain R [auth C] mmCIF format, chain P [auth B] mmCIF format, chain N [auth A] mmCIF format, chain JA [auth L] mmCIF format, chain HA [auth K] mmCIF format, chain FA [auth J] mmCIF format, chain DA [auth I] mmCIF format, chain BA [auth H]	BA [auth H] DA [auth I] FA [auth J] HA [auth K] JA [auth L] BA [auth H], DA [auth I], FA [auth J], HA [auth K], JA [auth L], N [auth A], P [auth B], R [auth C], T [auth D], V [auth E], X [auth F], Z [auth G]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain BA [auth H] Focus chain DA [auth I] Focus chain FA [auth J] Focus chain HA [auth K] Focus chain JA [auth L] Focus chain N [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain X [auth F] Focus chain Z [auth G] Interactions & Density Focus chain BA [auth H] Focus chain DA [auth I] Focus chain FA [auth J] Focus chain HA [auth K] Focus chain JA [auth L] Focus chain N [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain X [auth F] Focus chain Z [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.94 Å
R-Value Free: 0.274 (Depositor), 0.280 (DCC)
R-Value Work: 0.196 (Depositor), 0.200 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.371	α = 90
b = 154.161	β = 90
c = 328.864	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-05-22

Deposition Author(s):

Fellner, M.

Hausinger, R.P.

Hu, J.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CHE-1516126

Revision History (Full details and data files)

Version 1.0: 2019-05-22
Type: Initial release
Version 1.1: 2019-11-27
Changes: Author supporting evidence
Version 1.2: 2021-05-12
Changes: Database references, Derived calculations
Version 1.3: 2023-10-11
Changes: Data collection, Database references, Refinement description