4JN8 | pdb_00004jn8

Crystal structure of an enolase (putative galactarate dehydratase, target efi-500740) from agrobacterium radiobacter, bound sulfate, no metal ion, ordered active site

• PDB DOI: https://doi.org/10.2210/pdb4JN8/pdb

• Classification: LYASE
• Organism(s): Rhizobium rhizogenes K84
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-03-14 Released: 2013-04-03 
• Deposition Author(s): Vetting, M.W., Groninger-Poe, F., Bouvier, J.T., Wichelecki, D., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Stead, M., Hillerich, B., Love, J., Seidel, R.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: 1.40 Å
• R-Value Free: 
  0.146 (Depositor), 0.142 (DCC) 
• R-Value Work: 
  0.129 (Depositor), 0.126 (DCC) 
• R-Value Observed: 
  0.129 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of an enolase (putative galactarate dehydratase, target efi-500740) from agrobacterium radiobacter, bound sulfate, no metal ion, ordered active site

Vetting, M.W., Groninger-Poe, F., Bouvier, J.T., Wichelecki, D., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Stead, M., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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: 45.35 kDa 
• Atom Count: 3,810 
• Modeled Residue Count: 395 
• Deposited Residue Count: 395 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENOLASE	A	395	Rhizobium rhizogenes K84	Mutation(s): 0
UniProt
Find proteins for B9JNP7 (Rhizobium rhizogenes (strain K84 / ATCC BAA-868)) Explore B9JNP7  Go to UniProtKB:  B9JNP7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	J [auth A], K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.146 (Depositor), 0.142 (DCC) 
• R-Value Work:  0.129 (Depositor), 0.126 (DCC) 
• R-Value Observed: 0.129 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.044	α = 90
b = 124.044	β = 90
c = 114.64	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-03 
Deposition Author(s): Vetting, M.W., Groninger-Poe, F., Bouvier, J.T., Wichelecki, D., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Stead, M., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2013-04-03
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description