3CYJ

Crystal structure of a mandelate racemase/muconate lactonizing enzyme-like protein from Rubrobacter xylanophilus

• PDB DOI: https://doi.org/10.2210/pdb3CYJ/pdb

• Classification: ISOMERASE
• Organism(s): Rubrobacter xylanophilus DSM 9941
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-04-25 Released: 2008-05-06 
• Deposition Author(s): Bonanno, J.B., Freeman, J., Bain, K.T., Zhang, F., Bravo, J., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.292 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.243 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.245 (Depositor) 

Literature

Crystal structure of a mandelate racemase/muconate lactonizing enzyme-like protein from Rubrobacter xylanophilus.

Bonanno, J.B., Freeman, J., Bain, K.T., Zhang, F., Bravo, J., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

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

Macromolecule Content

• Total Structure Weight: 160.46 kDa 
• Atom Count: 11,364 
• Modelled Residue Count: 1,436 
• Deposited Residue Count: 1,488 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase/muconate lactonizing enzyme-like protein	A, B, C, D	372	Rubrobacter xylanophilus DSM 9941	Mutation(s): 0  Gene Names: Rxyl_2719
UniProt
Find proteins for Q1ASJ4 (Rubrobacter xylanophilus (strain DSM 9941 / JCM 11954 / NBRC 16129 / PRD-1)) Explore Q1ASJ4  Go to UniProtKB:  Q1ASJ4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A], H [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	E [auth A], G [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.292 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.243 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.245 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 193.1	α = 90
b = 193.1	β = 90
c = 113.483	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-06 
Deposition Author(s): Bonanno, J.B., Freeman, J., Bain, K.T., Zhang, F., Bravo, J., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-05-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references