3KCJ | pdb_00003kcj

Room temperature neutron structure of apo-D-Xylose Isomerase (refined jointly with X-ray structure 3KBJ)

• PDB DOI: https://doi.org/10.2210/pdb3KCJ/pdb

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


• Deposited: 2009-10-21 Released: 2010-09-29 
• Deposition Author(s): Kovalevsky, A.Y., Langan, P.

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Experimental Data Snapshot

• Method: NEUTRON DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.181 (Depositor) 
• R-Value Work: 
  0.173 (Depositor) 

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• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.187 (Depositor), 0.174 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.170 (DCC) 

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: 43.28 kDa 
• Atom Count: 3,302 
• 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  Gene Names: xylA EC: 5.3.1.5
UniProt
Find proteins for P24300 (Streptomyces pseudogriseolus) Explore P24300  Go to UniProtKB:  P24300

Experimental Data & Validation

Experimental Data

• Method: NEUTRON DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.181 (Depositor) 
• R-Value Work:  0.173 (Depositor) 

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.187 (Depositor), 0.174 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.170 (DCC) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.04	α = 90
b = 99.52	β = 90
c = 102.47	γ = 90

Software Package:

Software Name	Purpose
nCNS	refinement
RETREAT	data reduction
RETREAT	data scaling
nCNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-29 
Deposition Author(s): Kovalevsky, A.Y., Langan, P.

Revision History  

• Version 1.0: 2010-09-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-07-27
  Changes: Data collection
• Version 1.3: 2011-08-17
  Changes: Database references
• Version 1.4: 2017-11-01
  Changes: Refinement description
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references
• Version 1.6: 2024-04-03
  Changes: Refinement description