3V5C | pdb_00003v5c

Crystal structure of the mutant E234A of Galacturonate Dehydratase from GEOBACILLUS SP. complexed with Mg

• PDB DOI: https://doi.org/10.2210/pdb3V5C/pdb

• Classification: LYASE
• Organism(s): Paenibacillus sp. Y412MC10
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-12-16 Released: 2012-12-19 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Groninger-Poe, F., Gerlt, J.A., Almo, S.C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 
  0.216 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the mutant E234A of Galacturonate Dehydratase from GEOBACILLUS SP. complexed with Mg

Fedorov, A.A., Fedorov, E.V., Groninger-Poe, F., Gerlt, J.A., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 176.27 kDa 
• Atom Count: 13,728 
• Modeled Residue Count: 1,523 
• Deposited Residue Count: 1,568 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase/muconate lactonizing protein	A, B, C, D	392	Paenibacillus sp. Y412MC10	Mutation(s): 1  Gene Names: GYMC10_3367
UniProt
Find proteins for A0ACD6B8H0 (Geobacillus sp. (strain Y412MC10)) Explore A0ACD6B8H0  Go to UniProtKB:  A0ACD6B8H0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	F [auth A], J [auth B], K [auth B], M [auth C], N [auth C], O [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
MG	E [auth A], G [auth B], H [auth B], I [auth B], L [auth C], P [auth D], Q [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free:  0.216 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.271	α = 90
b = 65.863	β = 94.17
c = 151.218	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
BALBES	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-19 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Groninger-Poe, F., Gerlt, J.A., Almo, S.C.

Revision History  

• Version 1.0: 2012-12-19
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description