3QZA | pdb_00003qza

Joint neutron and X-ray structure of apo-D-Xylose Isomerase at pH=5.9

• PDB DOI: https://doi.org/10.2210/pdb3QZA/pdb

• Classification: ISOMERASE
• Organism(s): Streptomyces pseudogriseolus
• Mutation(s): No 


• Deposited: 2011-03-04 Released: 2011-08-17 
• Deposition Author(s): Kovalevsky, A.Y., Hanson, L., Langan, P.

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Experimental Data Snapshot

• Method: NEUTRON DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.280 (Depositor) 
• R-Value Work: 
  0.254 (Depositor) 
• R-Value Observed: 
  0.254 (Depositor) 

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• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.211 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.254 (Depositor) 

Starting Model: experimental

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: 43.29 kDa 
• Atom Count: 3,318 
• 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
D8U	B [auth A]	deuterium(1+) D GPRLSGONYQIRFK-DYCDLGHISA-N

Experimental Data & Validation

Experimental Data

• Method: NEUTRON DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.280 (Depositor) 
• R-Value Work:  0.254 (Depositor) 
• R-Value Observed: 0.254 (Depositor) 

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.211 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.254 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.908	α = 90
b = 99.503	β = 90
c = 102.971	γ = 90

Software Package:

Software Name	Purpose
nCNS	refinement
d*TREK	data scaling
d*TREK	data reduction
LAUENORM	data reduction
LAUENORM	data scaling

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: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2018-04-25
  Changes: Data collection
• Version 1.3: 2018-06-06
  Changes: Data collection, Experimental preparation, Refinement description
• Version 1.4: 2019-03-13
  Changes: Data collection
• Version 1.5: 2023-09-13
  Changes: Data collection, Database references, Refinement description