2PS2 | pdb_00002ps2

Crystal structure of putative mandelate racemase/muconate lactonizing enzyme from Aspergillus oryzae

• PDB DOI: https://doi.org/10.2210/pdb2PS2/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Aspergillus oryzae RIB40
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-05-04 Released: 2007-05-22 
• Deposition Author(s): Fedorov, A.A., Toro, R., Fedorov, E.V., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

Crystal structure of putative mandelate racemase/muconate lactonizing enzyme from Aspergillus oryzae.

Fedorov, A.A., Toro, R., Fedorov, E.V., Sauder, J.M., Burley, S.K., Almo, S.C.

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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 generated by PISA (software)

Biological Assembly 6  

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

Biological assembly 6 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 161.16 kDa 
• Atom Count: 11,750 
• Modelled Residue Count: 1,444 
• Deposited Residue Count: 1,484 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative mandelate racemase/muconate lactonizing enzyme	A, B, C, D	371	Aspergillus oryzae RIB40	Mutation(s): 0  Gene Names: AO090011000058
UniProt
Find proteins for Q2U1E8 (Aspergillus oryzae (strain ATCC 42149 / RIB 40)) Explore Q2U1E8  Go to UniProtKB:  Q2U1E8

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.865	α = 90
b = 94.865	β = 90
c = 330.673	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SHELXS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-22 
Deposition Author(s): Fedorov, A.A., Toro, R., Fedorov, E.V., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2007-05-22
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2012-10-24
  Changes: Structure summary
• Version 1.4: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.5: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.6: 2024-02-21
  Changes: Data collection, Database references