2PCE | pdb_00002pce

Crystal structure of putative mandelate racemase/muconate lactonizing enzyme from Roseovarius nubinhibens ISM

• PDB DOI: https://doi.org/10.2210/pdb2PCE/pdb

• Classification: LYASE
• Organism(s): Roseovarius nubinhibens ISM
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-03-29 Released: 2007-04-10 
• Deposition Author(s): Bonanno, J.B., Rutter, M., Bain, K.T., Lau, C., Ozyurt, S., Smith, D., Wasserman, S., 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: 2.00 Å
• R-Value Free: 
  0.250 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Literature

Crystal structure of putative mandelate racemase/muconate lactonizing enzyme from Roseovarius nubinhibens ISM

Bonanno, J.B., Rutter, M., Bain, K.T., Lau, C., Ozyurt, S., 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: 329.57 kDa 
• Atom Count: 23,281 
• Modeled Residue Count: 2,973 
• Deposited Residue Count: 3,088 
• 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, E, F, G, H	386	Roseovarius nubinhibens ISM	Mutation(s): 0
UniProt
Find proteins for A3SNG0 (Roseovarius nubinhibens (strain ATCC BAA-591 / DSM 15170 / ISM)) Explore A3SNG0  Go to UniProtKB:  A3SNG0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.250 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 168.688	α = 90
b = 174.413	β = 90
c = 108.586	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
DENZO	data reduction
CCP4	data scaling
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-10 
Deposition Author(s): Bonanno, J.B., Rutter, M., Bain, K.T., Lau, C., Ozyurt, S., 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: 2007-04-10
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2012-10-24
  Changes: Structure summary
• Version 1.4: 2017-10-18
  Changes: Refinement description
• Version 1.5: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.6: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.7: 2024-02-21
  Changes: Data collection, Database references