Macromolecule Content

Total Structure Weight: 751.32 kDa
Atom Count: 54924
Residue Count: 6448
Unique protein chains: 1

6LXV

Cryo-EM structure of phosphoketolase from Bifidobacterium longum

DOI: 10.2210/pdb6LXV/pdb
EMDataResource: EMD-30007

Classification: LYASE
Organism(s): Bifidobacterium longum subsp. longum F8
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-02-12 Released: 2021-02-17
Deposition Author(s): Nakata, K., Miyazaki, N., Yamaguchi, H., Hirose, M., Miyano, H., Mizukoshi, T., Kashiwagi, T., Iwasaki, K.
Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Literature

Cryo-EM structure of phosphoketolase from Bifidobacterium longum

Nakata, K., Miyazaki, N., Yamaguchi, H., Hirose, M., Miyano, H., Mizukoshi, T., Kashiwagi, T., Iwasaki, K.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoketolase	A, B, C, D, E, F, G, H	831	Bifidobacterium longum subsp. longum F8	Mutation(s): 0 Gene Names: BIL_11880 EC: 4.1.2.22
Find proteins for D6D942 (Bifidobacterium longum subsp. longum F8) Explore D6D942 Go to UniProtKB: D6D942
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TPP Query on TPP Download Ideal Coordinates CCD File SDF format, chain I [A] SDF format, chain K [B] SDF format, chain M [C] SDF format, chain O [D] SDF format, chain Q [E] SDF format, chain S [F] SDF format, chain U [G] SDF format, chain W [H] MOL2 format, chain I [A] MOL2 format, chain K [B] MOL2 format, chain M [C] MOL2 format, chain O [D] MOL2 format, chain Q [E] MOL2 format, chain S [F] MOL2 format, chain U [G] MOL2 format, chain W [H]	A, B, C, D, E, F, G, H	THIAMINE DIPHOSPHATE C₁₂ H₁₉ N₄ O₇ P₂ S AYEKOFBPNLCAJY-UHFFFAOYSA-O		Ligand Interaction
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain J [A] SDF format, chain L [B] SDF format, chain N [C] SDF format, chain P [D] SDF format, chain R [E] SDF format, chain T [F] SDF format, chain V [G] SDF format, chain X [H] MOL2 format, chain J [A] MOL2 format, chain L [B] MOL2 format, chain N [C] MOL2 format, chain P [D] MOL2 format, chain R [E] MOL2 format, chain T [F] MOL2 format, chain V [G] MOL2 format, chain X [H]	A, B, C, D, E, F, G, H	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Deposited Date: 2020-02-12
Released Date: 2021-02-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	--

Revision History

Version 1.0: 2021-02-17
Type: Initial release

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.