3BJS | pdb_00003bjs

Crystal structure of a member of enolase superfamily from Polaromonas sp. JS666

• PDB DOI: https://doi.org/10.2210/pdb3BJS/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Polaromonas sp. JS666
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-12-04 Released: 2007-12-18 
• Deposition Author(s): Patskovsky, Y., Bonanno, J.B., Ozyurt, S., Dickey, M., Sauder, J.M., Reyes, C., Groshong, C., Gheyi, T., Smith, D., Wasserman, S.R., Gerlt, J., 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: 2.70 Å
• R-Value Free: 
  0.263 (Depositor) 
• R-Value Work: 
  0.205 (Depositor) 
• R-Value Observed: 
  0.207 (Depositor) 

Literature

Crystal Structure of a Member of Enolase Superfamily from Polaromonas sp. JS666.

Patskovsky, Y., Bonanno, J.B., Ozyurt, S., Dickey, M., Sauder, J.M., Reyes, C., Groshong, C., Gheyi, T., Smith, D., Wasserman, S.R., Gerlt, J., 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: 93.48 kDa 
• Atom Count: 5,730 
• Modeled Residue Count: 746 
• Deposited Residue Count: 856 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase/muconate lactonizing enzyme	A, B	428	Polaromonas sp. JS666	Mutation(s): 0  Gene Names: Bpro_5118
UniProt
Find proteins for A0ACD6B899 (Polaromonas sp. (strain JS666 / ATCC BAA-500)) Explore A0ACD6B899  Go to UniProtKB:  A0ACD6B899

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.263 (Depositor) 
• R-Value Work:  0.205 (Depositor) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 274.64	α = 90
b = 274.64	β = 90
c = 274.64	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-18 
Deposition Author(s): Patskovsky, Y., Bonanno, J.B., Ozyurt, S., Dickey, M., Sauder, J.M., Reyes, C., Groshong, C., Gheyi, T., Smith, D., Wasserman, S.R., Gerlt, J., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2007-12-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, 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, Refinement description