5ZIG

The Structure of cellobiose 2-epimerase from Spirochaeta thermophila DSM 6192

PDB DOI: https://doi.org/10.2210/pdb5ZIG/pdb

Classification: ISOMERASE
Organism(s): Spirochaeta thermophila DSM 6192
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2018-03-15 Released: 2019-04-10
Deposition Author(s): Feng, Y.H., Yang, R.J., Andrew, J.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.267
R-Value Work: 0.196
R-Value Observed: 0.199

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The Structure of cellobiose 2-epimerase from Spirochaeta thermophila DSM 6192

Feng, Y.H., Yang, R.J., Andrew, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 184.17 kDa
Atom Count: 13,681
Modelled Residue Count: 1,605
Deposited Residue Count: 1,616
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellobiose 2-epimerase	A, B, C, D	404	Spirochaeta thermophila DSM 6192	Mutation(s): 0 Gene Names: STHERM_c00950 EC: 5.1.3.11
UniProt
Find proteins for E0RU15 (Spirochaeta thermophila (strain ATCC 49972 / DSM 6192 / RI 19.B1)) Explore E0RU15 Go to UniProtKB: E0RU15
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	E0RU15
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO (Subject of Investigation/LOI) Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth D]	E [auth A], F [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.267
R-Value Work: 0.196
R-Value Observed: 0.199
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.53	α = 90
b = 205.164	β = 104.26
c = 67.723	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-04-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-04-10
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references

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 R01GM133198.