8KA2

Crystal structure of the RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) from Vibrio vulnificus

PDB DOI: https://doi.org/10.2210/pdb8KA2/pdb

Classification: TOXIN
Organism(s): Vibrio vulnificus
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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.38 Å
R-Value Free: 0.322
R-Value Work: 0.286
R-Value Observed: 0.288

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) from Vibrio vulnificus

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

To be published.

Macromolecule Content

Total Structure Weight: 95.27 kDa
Atom Count: 5,848
Modelled Residue Count: 729
Deposited Residue Count: 838
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RDTND-RID CBD	A, B	419	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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2S3R7M0
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.38 Å
R-Value Free: 0.322
R-Value Work: 0.286
R-Value Observed: 0.288
Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 207.726	α = 90
b = 207.726	β = 90
c = 54.647	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-07-10

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2024-07-10
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 R01GM133198.