8IYR | pdb_00008iyr

The cryo-EM structure of cellobiose phosphorylase from Clostridium thermocellum in complex with phosphate

PDB DOI: https://doi.org/10.2210/pdb8IYR/pdb
EM Map EMD-35829: EMDB EMDataResource

Classification: TRANSFERASE
Organism(s): Acetivibrio thermocellus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-04-05 Released: 2024-04-10
Deposition Author(s): Iriya, S., Kuga, T., Sunagawa, N., Igarashi, K.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8IYR

This is version 1.0 of the entry. See complete history.

Literature

The cryo-EM structure of cellobiose phosphorylase from Clostridium thermocellum in complex with phosphate

Iriya, S., Kuga, T., Sunagawa, N., Igarashi, K.

To be published.

Macromolecule Content

Total Structure Weight: 187.93 kDa
Atom Count: 13,231
Modeled Residue Count: 1,620
Deposited Residue Count: 1,634
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellobiose phosphorylase	A, B	817	Acetivibrio thermocellus	Mutation(s): 0 Gene Names: cbp EC: 2.4.1.20
UniProt
Find proteins for Q8VP44 (Acetivibrio thermocellus) Explore Q8VP44 Go to UniProtKB: Q8VP44
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8VP44
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.2.1

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-04-10

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	22J12566

Revision History (Full details and data files)

Version 1.0: 2024-04-10
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.