3V5F | pdb_00003v5f

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

• PDB DOI: https://doi.org/10.2210/pdb3V5F/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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.195 (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)

Macromolecule Content 

• Total Structure Weight: 44.15 kDa 
• Atom Count: 3,451 
• Modeled Residue Count: 386 
• Deposited Residue Count: 392 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase/muconate lactonizing protein	A	392	Paenibacillus sp. Y412MC10	Mutation(s): 1  Gene Names: GYMC10_3367

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	D [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.986	α = 90
b = 122.853	β = 90
c = 134.263	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