9IR1 | pdb_00009ir1

Crystal structure of CTB10-M40BpA

PDB DOI: https://doi.org/10.2210/pdb9IR1/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Cercospora sp. JNU001
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-07-13 Released: 2025-07-16
Deposition Author(s): Fu, K., Rao, Y.J.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free:
0.226 (Depositor), 0.226 (DCC)
R-Value Work:
0.184 (Depositor), 0.186 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of CTB10-M40BpA

Fu, K., Rao, Y.J.

To be published.

Macromolecule Content

Total Structure Weight: 33.4 kDa
Atom Count: 2,264
Modeled Residue Count: 252
Deposited Residue Count: 282
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CTB10	A, B	141	Cercospora sp. JNU001	Mutation(s): 1
UniProt
Find proteins for A0A977K7H6 (Cercospora sp. JNU001) Explore A0A977K7H6 Go to UniProtKB: A0A977K7H6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A977K7H6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PBF Query on PBF	A, B	L-PEPTIDE LINKING	C₁₆ H₁₅ N O₃		PHE

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.226 (Depositor), 0.226 (DCC)
R-Value Work: 0.184 (Depositor), 0.186 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.326	α = 90
b = 65.581	β = 94.15
c = 49.183	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-07-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private	China	2021YFC2102700
Other private	China	BK20202002
Other private	China	KYCX20_1812
Other private	China	KYCX20_1816

Revision History (Full details and data files)

Version 1.0: 2025-07-16
Type: Initial release

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.