3TOY | pdb_00003toy

CRYSTAL STRUCTURE OF ENOLASE BRADO_4202 (TARGET EFI-501651) FROM Bradyrhizobium sp. ORS278 WITH CALCIUM AND ACETATE BOUND

• PDB DOI: https://doi.org/10.2210/pdb3TOY/pdb

• Classification: LYASE
• Organism(s): Bradyrhizobium sp. ORS 278
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-09-06 Released: 2011-09-21 
• Deposition Author(s): Patskovsky, Y., Kim, J., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammond, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.199 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.158 (Depositor) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: experimental

Literature

CRYSTAL STRUCTURE OF MANDELATE RACEMASE FROM Bradyrhizobium sp. ORS278

Patskovsky, Y., Kim, J., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammond, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., 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: 167.34 kDa 
• Atom Count: 12,537 
• Modeled Residue Count: 1,436 
• Deposited Residue Count: 1,532 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase/muconate lactonizing enzyme family protein	A, B, C, D	383	Bradyrhizobium sp. ORS 278	Mutation(s): 0  Gene Names: BRADO4202 EC: 5.1.2.2 (PDB Primary Data), 5.5.1.1 (PDB Primary Data)
UniProt
Find proteins for A0ACD6B9G9 (Bradyrhizobium sp. (strain ORS 278)) Explore A0ACD6B9G9  Go to UniProtKB:  A0ACD6B9G9

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P4C	H [auth A], M [auth B], N [auth B], R [auth C], S [auth C], X [auth D]	O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL C14 H28 O8 CTLLATPOKUEFSQ-UHFFFAOYSA-N
ACT	F [auth A], K [auth B], Q [auth C], V [auth D]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NI	G [auth A], L [auth B], W [auth D]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CA	E [auth A], I [auth A], J [auth B], O [auth B], P [auth C], T [auth C], U [auth D], Y [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.199 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.158 (Depositor) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.389	α = 90
b = 131.838	β = 90
c = 108.825	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-21 
Deposition Author(s): Patskovsky, Y., Kim, J., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammond, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2011-09-21
  Type: Initial release
  
• Version 1.1: 2012-02-22
  Changes: Database references, Structure summary
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description