4XKM

Crystal structure of Xylose Isomerase from an human intestinal tract microbe Bacteroides thetaiotaomicron

PDB DOI: https://doi.org/10.2210/pdb4XKM/pdb

Classification: ISOMERASE
Organism(s): Bacteroides thetaiotaomicron VPI-5482
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-01-12 Released: 2015-12-23
Deposition Author(s): Han, B.G., Bong, S.M., Cho, J.W., Lee, B.I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.211
R-Value Work: 0.186
R-Value Observed: 0.187

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a class 2 D-xylose isomerase from the human intestinal tract microbe Bacteroides thetaiotaomicron

Han, B.G., Bong, S.M., Cho, J.W., Kim, M.D., Kim, S.J., Lee, B.I.

(2015) Korean Soc Struct Biology 3: 41-47

Macromolecule Content

Total Structure Weight: 410.24 kDa
Atom Count: 30,000
Modelled Residue Count: 3,480
Deposited Residue Count: 3,664
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xylose isomerase	A, B, C, D, E A, B, C, D, E, F, G, H	458	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0 Gene Names: xylA, BT_0793 EC: 5.3.1.5
UniProt
Find proteins for Q8A9M2 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A9M2 Go to UniProtKB: Q8A9M2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8A9M2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth E] SDF format, chain R [auth E] SDF format, chain S [auth F] SDF format, chain T [auth F] SDF format, chain U [auth G] SDF format, chain V [auth G] SDF format, chain W [auth H] SDF format, chain X [auth H] SDF format, chain O [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth E] MOL2 format, chain S [auth F] MOL2 format, chain T [auth F] MOL2 format, chain U [auth G] MOL2 format, chain V [auth G] MOL2 format, chain W [auth H] MOL2 format, chain X [auth H] MOL2 format, chain O [auth D]	I [auth A] J [auth A] K [auth B] L [auth B] M [auth C] I [auth A], J [auth A], K [auth B], L [auth B], M [auth C], N [auth C], O [auth D], P [auth D], Q [auth E], R [auth E], S [auth F], T [auth F], U [auth G], V [auth G], W [auth H], X [auth H]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth G] Focus chain W [auth H] Focus chain X [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth G] Focus chain W [auth H] Focus chain X [auth H]