8JSK

Crystal structure of an N-terminal cyclic nucleotide-binding domain of a PycTIR from Pseudovibrio sp. in complex with cUMP

PDB DOI: https://doi.org/10.2210/pdb8JSK/pdb

Classification: SIGNALING PROTEIN
Organism(s): Pseudovibrio sp. W64
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-06-20 Released: 2024-07-03
Deposition Author(s): Wang, Y.-C., Yang, C.-S., Hou, M.-H., Chen, Y.
Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.244
R-Value Work: 0.198

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of an N-terminal cyclic nucleotide-binding domain of a PycTIR from Pseudovibrio sp. in complex with cUMP

Wang, Y.-C., Yang, C.-S., Hou, M.-H., Chen, Y.

To be published.

Macromolecule Content

Total Structure Weight: 36 kDa
Atom Count: 2,606
Modelled Residue Count: 316
Deposited Residue Count: 316
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PycTIR	A, B	158	Pseudovibrio sp. W64	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6SY (Subject of Investigation/LOI) Query on 6SY Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	Uridine-3',5'-cyclic monophosphate C₉ H₁₁ N₂ O₈ P NXIHNBWNDCFCGL-XVFCMESISA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.244
R-Value Work: 0.198
Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.485	α = 90
b = 133.485	β = 90
c = 34.069	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-07-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	111-2311-B-039-001-MY3

Revision History (Full details and data files)

Version 1.0: 2024-07-03
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.