2QQ6 | pdb_00002qq6

Crystal structure of mandelate racemase/muconate lactonizing enzyme-like protein from Rubrobacter xylanophilus DSM 9941

• PDB DOI: https://doi.org/10.2210/pdb2QQ6/pdb

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


• Deposited: 2007-07-26 Released: 2007-08-14 
• Deposition Author(s): Eswaramoorthy, S., Madegowda, M., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.282 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Literature

Crystal structure of mandelate racemase/muconate lactonizing enzyme-like protein from Rubrobacter xylanophilus DSM 9941.

Eswaramoorthy, S., Madegowda, M., Burley, S.K., Swaminathan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 91.3 kDa 
• Atom Count: 6,051 
• Modeled Residue Count: 790 
• Deposited Residue Count: 820 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase/muconate lactonizing enzyme-like protein	A, B	410	Rubrobacter xylanophilus DSM 9941	Mutation(s): 0  Gene Names: Rxyl_0547
UniProt
Find proteins for Q1AYK7 (Rubrobacter xylanophilus (strain DSM 9941 / JCM 11954 / NBRC 16129 / PRD-1)) Explore Q1AYK7  Go to UniProtKB:  Q1AYK7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.282 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 184.369	α = 90
b = 184.369	β = 90
c = 118.108	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SOLVE	phasing
SHARP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-14 
Deposition Author(s): Eswaramoorthy, S., Madegowda, M., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2007-08-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Structure summary