8HVJ | pdb_00008hvj

The structure of the E. coli mRNA endoonuclease YiCC

PDB DOI: https://doi.org/10.2210/pdb8HVJ/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-12-27 Released: 2023-12-27
Deposition Author(s): Xie, W., Hunag, L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.05 Å
R-Value Free:
0.385 (Depositor), 0.390 (DCC)
R-Value Work:
0.321 (Depositor), 0.320 (DCC)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

The structure of the E. coli mRNA endoonuclease YiCC

Xie, W., Hunag, L.

To be published.

Macromolecule Content

Total Structure Weight: 99.65 kDa
Atom Count: 6,285
Modeled Residue Count: 795
Deposited Residue Count: 861
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0701 protein YicC	A, B, C	287	Escherichia coli K-12	Mutation(s): 0 Gene Names: yicC, b3644, JW3619 EC: 3.1.26
UniProt
Find proteins for P23839 (Escherichia coli (strain K12)) Explore P23839 Go to UniProtKB: P23839
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P23839
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 4.05 Å
R-Value Free: 0.385 (Depositor), 0.390 (DCC)
R-Value Work: 0.321 (Depositor), 0.320 (DCC)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.208	α = 90
b = 77.158	β = 90
c = 102.596	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2023-12-27

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32271322

Revision History (Full details and data files)

Version 1.0: 2023-12-27
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 R01GM157729.