Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 84698.81 
• Atom Count: 5450 
• Residue Count: 782 
• Unique protein chains: 1

4E8G

Crystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans pd1222 (target nysgrc-012907) with bound mg

• DOI: 10.2210/pdb4E8G/pdb

• Classification: ISOMERASE
• Organism(s): Paracoccus denitrificans (strain Pd 1222)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2012-03-20 Released: 2012-05-02 
• Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Wasserman, S.R., Morisco, L.L., Sojitra, S., Chamala, S., Kar, A., Lafleur, J., Villigas, G., Evans, B., Hammonds, J., Gizzi, A., Zencheck, W.D., Hillerich, B., Love, J., Seidel, R.D., Bonanno, J.B., Gerlt, J.A., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.202 
• R-Value Work: 0.163 

Literature

Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine.

Kumar, R., Zhao, S., Vetting, M.W., Wood, B.M., Sakai, A., Cho, K., Solbiati, J., Almo, S.C., Sweedler, J.V., Jacobson, M.P., Gerlt, J.A., Cronan, J.E.

(2014) MBio 5: e00933-e00913

• PubMed: 24520058 
• DOI: 10.1128/mBio.00933-13
• Primary Citation of Related Structures:  
  4J1O, 4IZG

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein	A, B	391	Paracoccus denitrificans (strain Pd 1222)	Mutation(s): 0  Gene Names: hpbD EC: 5.1.1.22
Find proteins for A1B198 (Paracoccus denitrificans (strain Pd 1222)) Go to UniProtKB:  A1B198

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MG	A, 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 Å
• R-Value Free: 0.202 
• R-Value Work: 0.163 
• Space Group: P 4 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 117.963	α = 90.00
b = 117.963	β = 90.00
c = 111.154	γ = 90.00

Software Package:

Software Name	Purpose
SCALA	data scaling
PDB_EXTRACT	data extraction
PHENIX	refinement
MOSFLM	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-03-20 
• Released Date: 2012-05-02 
• Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Wasserman, S.R., Morisco, L.L., Sojitra, S., Chamala, S., Kar, A., Lafleur, J., Villigas, G., Evans, B., Hammonds, J., Gizzi, A., Zencheck, W.D., Hillerich, B., Love, J., Seidel, R.D., Bonanno, J.B., Gerlt, J.A., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Revision History 

• Version 1.0: 2012-05-02
  Type: Initial release
• Version 1.1: 2018-01-24
  Type: Database references