5XB6 | pdb_00005xb6

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 (Depositor), 0.220 (DCC)
R-Value Work:
0.182 (Depositor), 0.184 (DCC)
R-Value Observed:
0.184 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5XB6

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
Modeled Residue Count: 3,671
Deposited Residue Count: 3,672
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 (Depositor), 0.220 (DCC)
R-Value Work: 0.182 (Depositor), 0.184 (DCC)
R-Value Observed: 0.184 (Depositor)

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

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View more in-depth experimental data

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

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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.