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
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wwPDB Validation 3D Report Full Report

Validation slider image for 9IR1

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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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

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View more in-depth experimental data

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

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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.