8YRI | pdb_00008yri

Crystal structure of sugar phosphotransferase system EIIB component CPF_0401 from Clostridium perfringens

PDB DOI: https://doi.org/10.2210/pdb8YRI/pdb

Classification: TRANSFERASE
Organism(s): Clostridium perfringens ATCC 13124
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-03-21 Released: 2025-04-16
Deposition Author(s): Hirayama, Y., Oiki, S., Mikami, B., Ogura, K., Hashimoto, W.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.257 (Depositor), 0.257 (DCC)
R-Value Work:
0.215 (Depositor), 0.215 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8YRI

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

Literature

Crystal structure of sugar phosphotransferase system EIIB component CPF_0401 from Clostridium perfringens

Hirayama, Y., Oiki, S., Mikami, B., Ogura, K., Hashimoto, W.

To be published.

Macromolecule Content

Total Structure Weight: 38.27 kDa
Atom Count: 2,468
Modeled Residue Count: 288
Deposited Residue Count: 336
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PTS system, mannose/fructose/sorbose family, IIB component	A, B	168	Clostridium perfringens ATCC 13124	Mutation(s): 0 Gene Names: CPF_0401
UniProt
Find proteins for A0A0H2YUZ2 (Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A)) Explore A0A0H2YUZ2 Go to UniProtKB: A0A0H2YUZ2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2YUZ2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		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: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.257 (Depositor), 0.257 (DCC)
R-Value Work: 0.215 (Depositor), 0.215 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.253	α = 90
b = 69.811	β = 90.25
c = 61.863	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-04-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	21H02156

Revision History (Full details and data files)

Version 1.0: 2025-04-16
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.