7SEU | pdb_00007seu

Crystal structure of E coli contaminant protein YncE co-purified with a plant protein

PDB DOI: https://doi.org/10.2210/pdb7SEU/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Escherichia coli
Mutation(s): No

Deposited: 2021-10-01 Released: 2022-04-20
Deposition Author(s): Chai, L., Zhu, P., Chai, J., Pang, C., Andi, B., McsWeeney, S., Shanklin, J., Liu, Q.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.256 (Depositor), 0.260 (DCC)
R-Value Work:
0.236 (Depositor), 0.240 (DCC)
R-Value Observed:
0.237 (Depositor)

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

This is version 1.1 of the entry. See complete history.

Literature

AlphaFold Protein Structure Database for Sequence-Independent Molecular Replacement

Chai, L., Zhu, P., Chai, J., Pang, C., Andi, B., McSweeney, S., Shanklin, J., Liu, Q.

(2021) Crystals (Basel) 11

DOI: https://doi.org/10.3390/cryst11101227

Macromolecule Content

Total Structure Weight: 154.66 kDa
Atom Count: 10,124
Modeled Residue Count: 1,279
Deposited Residue Count: 1,412
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PQQ-dependent catabolism-associated beta-propeller protein	A, B, C, D	353	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P76116 (Escherichia coli (strain K12)) Explore P76116 Go to UniProtKB: P76116
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P76116
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.256 (Depositor), 0.260 (DCC)
R-Value Work: 0.236 (Depositor), 0.240 (DCC)
R-Value Observed: 0.237 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.172	α = 90
b = 147.27	β = 104.4
c = 96.899	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-04-20

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--
Department of Energy (DOE, United States)	United States	--

Revision History (Full details and data files)

Version 1.0: 2022-04-20
Type: Initial release
Version 1.1: 2024-04-03
Changes: Data collection, Refinement description

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.