9ILD | pdb_00009ild

Complex structure of Cap3 and CD-NTase

PDB DOI: https://doi.org/10.2210/pdb9ILD/pdb

Classification: ANTIFUNGAL PROTEIN
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-06-29 Released: 2024-07-31
Deposition Author(s): Li, F.Q., Ma, W.F.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free:
0.283 (Depositor), 0.290 (DCC)
R-Value Work:
0.228 (Depositor), 0.232 (DCC)
R-Value Observed:
0.233 (Depositor)

Starting Model: in silico
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Literature

Structural and functional characterization of the bacterial Cap3 enzyme in deconjugation and regulation of the cyclic dinucleotide transferase CD-NTase

Li, F.Q., Ma, W.F.

To be published.

Macromolecule Content

Total Structure Weight: 21.09 kDa
Atom Count: 1,481
Modeled Residue Count: 178
Deposited Residue Count: 183
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase	A	156	Escherichia coli	Mutation(s): 0 Gene Names: GOP25_26465 EC: 3.4
UniProt
Find proteins for P0DTF3 (Escherichia coli (strain TW11681)) Explore P0DTF3 Go to UniProtKB: P0DTF3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTF3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic GMP-AMP synthase	B	27	Escherichia coli	Mutation(s): 0 Gene Names: ETECE562_01214 EC: 2.7.7
UniProt
Find proteins for P0DTF0 (Escherichia coli (strain TW11681)) Explore P0DTF0 Go to UniProtKB: P0DTF0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTF0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN 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]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free: 0.283 (Depositor), 0.290 (DCC)
R-Value Work: 0.228 (Depositor), 0.232 (DCC)
R-Value Observed: 0.233 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.051	α = 90
b = 54.843	β = 90
c = 59.606	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-07-31

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government		--

Revision History (Full details and data files)

Version 1.0: 2024-07-31
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.