3QYS

Room Temperature X-ray Structure of D-Xylose Isomerase in complex with 0.6Ni2+ cation bound in M2 metal binding site at pH=5.8

PDB DOI: https://doi.org/10.2210/pdb3QYS/pdb

Classification: ISOMERASE
Organism(s): Streptomyces rubiginosus
Mutation(s): No

Deposited: 2011-03-03 Released: 2011-08-17
Deposition Author(s): Kovalevsky, A.Y., Hanson, L., Langan, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.217
R-Value Work: 0.171

wwPDB Validation 3D Report Full Report

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

Literature

Identification of the Elusive Hydronium Ion Exchanging Roles with a Proton in an Enzyme at Lower pH Values.

Kovalevsky, A.Y., Hanson, B.L., Mason, S.A., Yoshida, T., Fisher, S.Z., Mustyakimov, M., Forsyth, V.T., Blakeley, M.P., Keen, D.A., Langan, P.

(2011) Angew Chem Int Ed Engl 50: 7520-7523

PubMed: 21604345 Search on PubMed
DOI: https://doi.org/10.1002/anie.201101753
Primary Citation of Related Structures:
3KBJ, 3KCJ, 3QYS, 3QZA

Organizational Affiliation

Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA. ayk@lanl.gov

Macromolecule Content

Total Structure Weight: 43.34 kDa
Atom Count: 3,348
Modelled Residue Count: 388
Deposited Residue Count: 388
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	388	Streptomyces rubiginosus	Mutation(s): 0 EC: 5.3.1.5
UniProt
Find proteins for P24300 (Streptomyces rubiginosus) Explore P24300 Go to UniProtKB: P24300
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P24300
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.217
R-Value Work: 0.171
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.9	α = 90
b = 99.63	β = 90
c = 102.84	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHELX	model building
SHELXL-97	refinement
d*TREK	data reduction
d*TREK	data scaling
SHELX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-08-17

Deposition Author(s):

Kovalevsky, A.Y.

Revision History (Full details and data files)

Version 1.0: 2011-08-17
Type: Initial release
Version 1.1: 2024-02-21
Changes: Data collection, Database references, Derived calculations

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.