3QYS | pdb_00003qys

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 pseudogriseolus
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.217 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.157 (DCC) 

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 
• DOI: https://doi.org/10.1002/anie.201101753
• Primary Citation Related Structures: 
  3KBJ, 3KCJ, 3QYS, 3QZA

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Organizational Affiliation: 
• Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 43.34 kDa 
• Atom Count: 3,348 
• Modeled Residue Count: 388 
• Deposited Residue Count: 388 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xylose isomerase	A	388	Streptomyces pseudogriseolus	Mutation(s): 0  EC: 5.3.1.5
UniProt
Find proteins for P24300 (Streptomyces pseudogriseolus) Explore P24300  Go to UniProtKB:  P24300

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.217 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.157 (DCC) 

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

Entry History 

Deposition Data

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

Revision History  

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