8KA1

Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-free calmodulin

• PDB DOI: https://doi.org/10.2210/pdb8KA1/pdb

• Classification: TOXIN
• Organism(s): Vibrio vulnificus, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-08-02 Released: 2024-07-10 
• Deposition Author(s): Lee, Y., Choi, S., Hwang, J., Kim, M.H.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.82 Å
• R-Value Free: 0.342 
• R-Value Work: 0.271 
• R-Value Observed: 0.275 

Starting Model: experimental

Literature

Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-free calmodulin

Lee, Y., Choi, S., Hwang, J., Kim, M.H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 259.18 kDa 
• Atom Count: 17,066 
• Modelled Residue Count: 2,136 
• Deposited Residue Count: 2,268 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RDTND-RID CBD	A, C, E, G	416	Vibrio vulnificus	Mutation(s): 0  Gene Names: CRN52_02910 EC: 3.4.22
UniProt
Find proteins for A0A2S3R7M0 (Vibrio vulnificus) Explore A0A2S3R7M0  Go to UniProtKB:  A0A2S3R7M0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin-2	B, D, F, H	151	Homo sapiens	Mutation(s): 0  Gene Names: CALM2, CAM2, CAMB
UniProt & NIH Common Fund Data Resources
Find proteins for P0DP24 (Homo sapiens) Explore P0DP24  Go to UniProtKB:  P0DP24
PHAROS:  P0DP24 GTEx:  ENSG00000143933

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	I [auth F], J [auth F], K [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, C, E, G	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.82 Å
• R-Value Free: 0.342 
• R-Value Work: 0.271 
• R-Value Observed: 0.275 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.032	α = 90
b = 88.081	β = 90.14
c = 136.954	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-10 
Deposition Author(s): Lee, Y., Choi, S., Hwang, J., Kim, M.H.

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Funding Organization	Location	Grant Number
Other government	Korea, Republic Of	the Korea Research Institute of Bioscience and Biotechnology (KRIBB) Research Initiative Program (KGM1382312)
Other government	Korea, Republic Of	the Korea Research Institute of Bioscience and Biotechnology (KRIBB) Research Initiative Program (KGM2112335)

Revision History  

• Version 1.0: 2024-07-10
  Type: Initial release