5XB6

Crystal structure of YcjY from E. Coli

PDB DOI: https://doi.org/10.2210/pdb5XB6/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-03-16 Released: 2018-04-11
Deposition Author(s): Chen, C.F., Gao, Z.Q., Liu, Q.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.219
R-Value Work: 0.182
R-Value Observed: 0.184

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of YcjY from E. Coli

Chen, C.F., Gao, Z.Q., Liu, Q.S.

To be published.

Macromolecule Content

Total Structure Weight: 404.26 kDa
Atom Count: 32,624
Modelled Residue Count: 3,671
Deposited Residue Count: 3,672
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein YcjY	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	306	Escherichia coli K-12	Mutation(s): 0 Gene Names: ycjY, b1327, JW5804
UniProt
Find proteins for P76049 (Escherichia coli (strain K12)) Explore P76049 Go to UniProtKB: P76049
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P76049
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.219
R-Value Work: 0.182
R-Value Observed: 0.184
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.584	α = 90
b = 216.405	β = 90
c = 258.839	γ = 90

Software Package:

Software Name	Purpose
PHENIX	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: 2018-04-11

Deposition Author(s):

Funding Organization	Location	Grant Number
	China	--

Revision History (Full details and data files)

Version 1.0: 2018-04-11
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.