3RRA | pdb_00003rra

Crystal structure of enolase PRK14017 (target EFI-500653) from Ralstonia pickettii 12J with magnesium bound

• PDB DOI: https://doi.org/10.2210/pdb3RRA/pdb

• Classification: LYASE
• Organism(s): Ralstonia pickettii 12J
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-04-29 Released: 2011-05-11 
• Deposition Author(s): Patskovsky, Y., Ramagopal, U.A., Hillerich, B., Seidel, R.D., Zencheck, W.D., Toro, R., 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: 2.30 Å
• R-Value Free: 
  0.263 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of enolase PRK14017 from Ralstonia pickettii

Patskovsky, Y., Ramagopal, U.A., Hillerich, B., Seidel, R.D., Zencheck, W.D., Toro, R., 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: 90.26 kDa 
• Atom Count: 5,970 
• Modeled Residue Count: 753 
• Deposited Residue Count: 810 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative D-galactonate dehydratase	A, B	405	Ralstonia pickettii 12J	Mutation(s): 0  Gene Names: dgoD, Rpic_2990 EC: 4.2.1.6
UniProt
Find proteins for B2UCA8 (Ralstonia pickettii (strain 12J)) Explore B2UCA8  Go to UniProtKB:  B2UCA8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.263 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.339	α = 90
b = 117.339	β = 90
c = 113.685	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: 2011-05-11 
Deposition Author(s): Patskovsky, Y., Ramagopal, U.A., Hillerich, B., Seidel, R.D., Zencheck, W.D., Toro, R., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2011-05-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary